I was able to kill Firkraag upon our first meeting, which apparently breaks the Paladin Stronghold quest, as you will not get the quest to kill him, the extra exp for turning it in, or the stronghold. The man you're supposed to talk to just says "we'll send for you". Supposedly this was also an issue in original BG2, but I don't remember. At any rate, it can be fixed really easily I would think by just adding a line of dialogue (ie. "I heard Firkraag was defeated, etc etc") once you're finished with the third quest.
I did Anomen's promotion quest, and he was named "Sir Anomen" in his character card. However, Keldorn has been a knight the entire time and doesn't have his prefix... Not a big deal, but it's goofy.
Also, I've noticed Gauth and Beholders are still a problem. They machinegun their blasts (I guess their basic attack?) at pretty much everything in range, and it's terrible. Thankfully not such a big deal if you have a certain shield, but still.