Basically, any script, I've noticed.
On the ship where the hooded figure is scripted to cast that spell on your ship, it will actually skip the character's turn who is first to act. For example, Ifan had the highest initiative, and his turn that round was completely lost.
In mordus's lich dungeon, the vases that transform. There's a script that will turn the vases into the undead that you fight. This event forcibly skips the person who is first in initiative order.
Any event where the enemy transforms before combat proceeds, for example against the doctor. It forcibly skips the first turn of whoever is going first.
I don't need to explain how bad this is, especially when the character you invested all those wits points really needs to go first.