A lot of things, but most of them stem from the expansion being very clearly rushed to release. The narrative was also incomplete, and Bungie had to add a bunch of supplemental lore to the seasonal missions instead of putting them in the main campaign where it belongs.

Traditionally, Bungie keeps the seasonal storyline separated from the campaign story, because they're technically separate purchases the player has to make, so it makes sense to keep those stories apart from each other, so that a player who only buys the expansions but not the season passes won't be missing out on any narrative threads that they haven't already invested time and money into.

Unfortunately, that wasn't the case with Lightfall. The campaign didn't finish telling the story, and spent about half of the campaign time sending the player on a search for a MacGuffin that the game never properly explains, and the other half was spent awkwardly learning how to use the new Strand subclass. Except all the campaign missions where you get to experiment with Strand gave you a super-boosted version of the subclass which isn't available in normal play, so players were disappointed with how Strand performed in the endgame when it felt so overpowered during the campaign. A lot of the unanswered questions from the Lightfall campaign got explained in seasonal cutscenes, instead.

Now, granted, the seasonal and campaign stories are part of the same over-arching plot, so it's expected for there to be some overlap. But it's not supposed to go to the point where you literally can't understand the point of what you did during the campaign until 3 months after the campaign was released, and only if you also bought the season pass. They introduced "The Veil" in the Lightfall campaign, and it was never made clear to the player what it actually was or what it meant as far as the story goes, until some Season of the Deep cutscenes came out.

There's also the issue of Strand being completely reworked from whatever "poison" subclass it was originally going to be, and there's a lot of evidence from the Witch Queen campaign that suggests that the subclass was originally going to be poison (some unredacted text in the game originally referred to poisonous status effects for Strand that are not in the final version). Strand was originally going to be included in Witch Queen, but was cut and pushed back to Lightfall, and in its place in Witch Queen was a really half-baked mechanic called "Deepsight", which reveals hidden platforms for the player to use to progress through the stages (in places where it's clear that the player was originally expected to use the Strand grapple mechanic to progress).

To Bungie's credit, they've made some improvements to Lightfall since release, and it is in a much better state than it was when it launched. But the narrative issues are still there.