There are a lot possibilities for the difference:
- You can only do one of "Acorns" and "Security," not both.
- "Mass For The Pious," quest #100, isn't a quest any more. The quest numbers were not changed when that happened, it would be a lot of work and risks borking a lot of player saves.
- If you already have the pass to see the Witch when you encounter the guards, the quest "Check Point" never starts. This has no effect on gameplay and doesn't count as a failed quest.
- If you chose 'no cucking' during "Get Past Granny," the quest "Werewolf Hunt" never happens.
- There's several Side quests which can get missed without stalling things out. Example: If you didn't ask for sex with Vixenatrix after she announced her pregnancy, the quest "Bring The Lady A Gift" doesn't start. And if you stole the magic gem you are locked out from that quest entirely.