I was surprised by how much of this I actually missed having played through the game so much (and thinking I was paying lots of attention). I also feel like I have read quite a bit outside of the game itself, but completely missed the interactions between The Queen and the Nine... Had no idea she gave them Skolas and they let him free... Is this explicit in HoW (or the Grimoire) and I just missed it?

In game during the mission where you fight the Silent Fang outside the Cosmodrome wall Petra mentions that Skolas had been given to The Nine and wonders in awe how he could have escaped them. Listen as you start getting close to the the outside... I think the dialogue happens in that long narrow room lit red by the big red windows. That The Nine actively released him instead of him escaping is not touched on at all I don't think.

In the Grimoire, the whole story stretches all over the place. The Queen gives The Nine Skolas in what seemed to be compensation or appeasement for her forces crossing into their territory. The Nine then order Xur or someone like him release Skolas and give him a Ketch to command basically turning him lose against The Queen. It's also mentioned that perhaps the Queen is being friendly to the Guardians now because she wants to have an advantage if she is forced into war with The Nine. After you help her recapture Skolas she does learn that The Nine were behind his rampage...

I was sad that the article left out the theory that the Exo Stranger is one of the Ishtar Collective scientists who was trapped in a Vex simulation. See this thread for speculation on that.

Gameinformer has dropped a very story heavy article on Destiny. They say that the info is from the game story, grimoire and conversations with Bungie. They also say that all the info has been approved by Bungie as canon...

All of it? Even the speculation, fan theories, and apparent errors?

No, not all of it. At the very end of the first page they say:

We’ve made a point to fact-check our entire story directly with Bungie prior to publication; as such, we hope this can be an accurate and authoritative glimpse into the existing narrative. Anything not confirmed by Bungie is clearly described as such in the text.

and they thank Bungie again for sitting down with them at the end, and some things are marked as not confirmed, so I assume everything that isn't has been confirmed.
Were there things not marked out as theory that are inaccurate?

I'm going to go back and start looking closely now, but the point is, I don't like the Deep Throat approach to this. I'd much prefer that everything explicitly vetted by Bungie be sourced and quoted, or at least paraphrased, and then I'd know that everything else came from other sources or from the author, because that's what I normally assume anyway.

The situation we've got now is that what the reader thinks is meant by something might be slightly different from what the author intended which might also be slightly different from what a Bungie person thought was meant by it when they signed off on it, and since there are no direct quotes, who the heck knows?

and they thank Bungie again for sitting down with them at the end, and some things are marked as not confirmed, so I assume everything that isn't has been confirmed.
Were there things not marked out as theory that are inaccurate?

I have doubts about this:

In a heroic last stand that defies its previous encounters with the Darkness, the Traveler fights back rather than abandoning humanity.

I do sincerely hope Bungie isn't going down the "humanity is special in the cosmos" route that Halo ended up with. That is deeply disappointing if true. If not true, then either the author is overreaching or Bungie is deliberately concealing in order to set up a surprise later.

First, the strike team tracks down an exiled and disgraced warlock named Toland, who had been banished for investigating the Darkness and the Hive with a little more fervor than the Vanguard would have liked. In addition to being the guy who knows more about the Hive than anyone else, he is also famous for wielding a deadly and dark pulse rifle called Bad Juju.

Toland's mistake was going up against Crota with Bad Juju instead of Red Death. Assuming one has a pulse rifle fetish, that is.

In particular, at least some part of the conflict arises from the Vex possession of a fragment of the Darkness, which is hidden in a place called the Black Garden, a vast Vex sanctuary locked away on Mars in some forgotten corner of time.

I was going to call this out because of a little conflict I see between "heart" and "fragment" but in retrospect this is a matter of perspective-- for the Vex, their darkness fragment is the "heart of the Black Garden", so it's more important to them than it would be to the Darkness itself, hence the relative inequality in importance between "heart" and "fragment".

One would have thought, though, if this was the case, that the Stranger would know about it. I guess she didn't have time to explain.

The Vex completely overtake Mercury and transform it into a stronghold world, and they start to do the same on Venus, setting up a massive Citadel and beginning to overtake the ruins of humanity’s abandoned colony there.

This strikes me as just straight-up wrong. In game we're told the ruins on Venus are billions of years old, and that includes the Citadel location. Those were ruins when the Golden Age brought humans to Venus, which is long before the Vex return. The Citadel might be being reclaimed, but it isn't being "set up".

The Vex are contriving to conquer and infect reality across all time, hoping to carve themselves into the fabric of the universe. They create the Vault of Glass on Venus in an effort to unite their efforts in the past, present, and future.

Of course it's always difficult to handle tense when talking about time-travel, but this is potentially misleading, making it sounds as if the Vault was set up on Venus post-Golden Age, instead of making it part of the ruins, like the Citadel. Either the Vault was on Venus back when Venus looks like Mars does now, which was a long, long time ago, or else it sits outside of time and space entirely, neither of which is inferred by the way this is written.

Amidst all this, a number of Awoken and Fallen make names for themselves, but one of the most important is a woman named Petra Venj. She rises up from being a soldier in the Awoken army to one of the Queen’s lieutenants, striking numerous victories for her people. In her eagerness to wipe out the Fallen, at one point she calls in an airstrike on some Fallen, not realizing that several of Earth’s Guardians would also be hit and killed, along with their Ghosts. The mistake causes serious tensions between the Awoken and the Guardians on Earth. As penance, Petra is made emissary to the Tower, a role she detests.

This is utterly and indisputably at odds with the voice performance of Petra. She detests bureaucratic work back on the Reef, not working with Guardians. If anything, all during HoW she shows favor towards Guardians and makes sly jabs at Variks.

the Stranger shows up looking for a Guardian to help her thwart the plans of the Vex. She seems to be looking specifically for you, as she shows up right after you’re brought back from the dead, and she secretly follows your subsequent adventures.

This is where I have a problem with the choice of words and the "Bungie has confirmed everything we don't exempt" stance of the article. The author uses "seems" here to indicate they don't know if the Stranger is looking specifically for the player character or not. Presumably Bungie approved this word choice. But they know whether the Stranger was looking for the player or not, so either they're actually refusing to confirm this fact in an article that says everything not exempted is confirmed, or they want to continue to deliberately conceal the Stranger's motives in order to maintain suspense, even while giving the appearance of confirming canonical information.

The author either should not have backed off the assertion by using the word "seems" and gotten Bungie to confirm what the Stranger was looking for, or, failed that, should have removed the assertion entirely so as to avoid ambiguity.

On the bright side, by opening up the passageways into the underground, you finally give poor Eris Morn a chance to escape, and she starts to make her way back to the Tower. You also manage to track down and return a broken shard of the Traveler, which the Hive are using to drain Light from the Traveler.

Out of those two missions, I know which one we got to play, and which one I'd have rather played.

You proceed back to Venus, and get one of these eyes, and then return to the asteroid belt to acknowledge the Awoken Queen’s help, and glean the location of the Black Garden.

Huh? Nobody gleans nothing. Uldren and Sov knew all along, and they give you precise coordinates. They mock you in a prior cutscene for not even knowing where it is. Being unable to correctly characterize information given explicitly in cutscene dialogue does not inspire confidence in the author's ability to convey everything else that is essentially deep background.

To add insult to injury, you then get together with several of your fellow guardians, enter Crota’s dark dimensional hide-out, and destroy his body. In fact, to do so, you take his own sword and hack him apart with it.

I'm really just pointing out the inaccuracy of the game, not the article here, but the Sword of Crota was already destroyed. We get multiple swords from swordbearers, and plus Crota wields his own sword-- one that is appropriate scale to his oversized body.

Somebody somewhere at Bungie fell in love with this "killed him with his own sword" meme and now they've gotten stuck with it, but it just isn't so. I blame Luke Smith.

Why doesn’t the Queen just have you kill him in the first place?

That’s unclear. The Queen is inscrutable sometimes. It’s possible that she wants Skolas to die in disgrace and embarrassment.

Or else because this limits discontinuity between those who played only the main story missions and those that do the endgame activities like Raids and PoE.

In the vanilla game, there's no discontinuity, really, because those endgames have separate bosses. The main objective in the Vex plot in the vanilla game aims at the Heart of the Black Garden, and not at Atheon and the Vault of Glass, which get only a side mention in one Venus mission.

In the Dark Below, though, Crota remains unfinished business if you don't do the raid.

In HoW you can rest easy knowing that Skolas is back in prison, even if you don't go in there to try and kill him. The prison is just weird, anyway, though. The idea of a gladiatorial arena is fine, but the boss idea just breaks it.

an amusing little story about some human scientists on Venus who can’t figure out if they’re real or trapped in a Vex simulation of reality. But most of that is entirely ancillary to the actual narrative.

If the Vex are either the real big bad, or more closely tied to the Darkness than the others, then this might not really be ancillary. It certainly seems to connect to what goes on in the Vault.