The lack of options: The GM let us know afterwards that every time we thought we had a choice, we hadn't chosen wrong... he'd just been supposed to give us the illusion of choice. What was the point of that?
The River Drake fight: I (a level 1 paladin) almost died at this point. I was the first person to be hit by the Drake's breath weapon, which kept me stuck there for the rest of the fight, and after, since there was no duration on the effect. It took the entire effort of the party to get me out before I died from a monster that had died 8 rounds before.
The second prestige point: We nailed the first condition (the bluff check, due to a very deceitful gnome), but we missed the second one, the Perception Check, because we decided to use our Take 10 Perceptions, and it required higher. That was all us, but the third condition is the one that frustrated us. Before we left the boat, we were told by both merchants to avoid violence, so we took that to heart. When we fought the "priestess," we stabilized her, woke her back up, explained that it was all a misunderstanding, and brought her back inside the inn. We then found out that since we didn't cut her throat or kidnap her as she lay there, we lost the point. We still haven't figured out why we were advised by our passengers to not get the point.