• Cazador's Mansion entrance is through some kind of ramparts in Lower City. You only learn about Cazador from Astarion's quest (and those Gur people I think), then you most likely kill him right after meeting him in his dungeon. This quest doesn't tie into main story whatsoever.

Based on some speculation (of course there's no way to find out what were Larian's true plans for this character), Cazador was meant to be a politically important figure in Upper City, and possibly had more related quests. If devs dropped this idea, that would explain how Cazador became a random boss enounter that doesn't really have any impact outside of Astarion's quest. It also makes sense why entering his place is so weird.

• Gortash's coronation takes place in Wyrm's Rest, a military fortress of the Flaming Fist and not, you know, High Hall where the parliament and other members of Baldur's Gate upper crust (ahem Cazador) plot their political intrigues. Also Gortash doesn't even get a Chosen's form like Orin or Ketheric during their fights.

• Omeluum's ring, which was supposed to protect you from Absolute's influence, has been at some point turned into an anti-charm item. In EA it used to block your illithid powers, but they've been reworked since. The dialog doesn't really reflect that.

• Kithrak Voss gains some battle scars and loses a part of his ear when you meet him later. AFAIK this is not explained at all in the game. Apparently it's a relic of a now removed fight between Orin and Githyanki in the creche.

• That Iron Flask quest with a trapped spectator has a lackluster resolution, possibly because it was related to Upper City at some stage of development.

Edit:

• Infernal Iron, Enriched Infernal Iron, Soul Coins that have very little use

• Gold, Silver, Bronze bars and a bunch of other items that feel like they should be useful for crafting

• All the talk about 'consequences' of using tadpole powers. No, actually there are no consequences.