There is a questline that was accidentally left out of the final game due to a misnamed file. "A Test of Determination" is a questline for the Vampire Clan where the given objective is to confront a Daedra in the local dungeon where it lives over the control the player's bloodline has in a given region. The binary file is named P0B1XL08.QBN and the text-file is named P0B10L08.QRC. As a result of this oversight, the player can never get this quest unless you change the name of one file so that it matches the name of the other.
Queen Barenziah is incorrectly depicted as a Breton in the game, despite the lore depicting her as a Dark Elf. This was later corrected in the next game, Morrowind, where she makes an appearance in the Tribunal expansion.
It was originally planned for the player to have sex with NPCs in the game, and there is plenty of unused text in the game's code to reflect this. In addition to this, there's text suggesting you were originally able to join the prostitutes guild and turn your character into a prostitute.