Dagmung Wind-Whisker has the topic "gone missing" before you actually deliver the potions to him on a quest (Delivery for Dagmund). The delivery is also made by selecting a topic "Icebreaker Keep" which is strange and unintuitive.
In the "Letter of the Law" quest you're supposed to find goblets in the egg miner's boat, but there are no goblets to be found. No amount of taking, placing or eating the eggs led to the appearance of a dialogue topic with the miner. You're unable to confront the miner about the eggs, which forfeits the final questline reward.
In the next quest, "Writ for Counterfeit," the counterfeiters in the sewers attack on sight. No indication is given that there will be dialogue options with them if they're calmed. This forfeits the second bonus and the final reward.
If you become a vampire of a different clan than Orlukh, then complete the "Iron and Blood" quest while wearing Namira's Shroud, Budak will still offer you his blood as a reward. However, you won't turn into a vampire (at least on OpenMW), and your Porphyric Hemophilia will remain forever. Since Namira's Shroud script is currently broken (as far as I know), I don't know how it could be fixed. Maybe just add one more dialogue entry, filtered for PCVampire == 1.
'Sehutu' dialog doesn't change after killing the wizard. People in Volenfaryon still say that "He seems to be growing bolder with his raids". This line is spoken even by Agarinnu, who knows about the wizard's death.
