Perhaps this little nitpicking gripe shall come as sounding overly grumpy and unforgiving of the game, but for what its worth, here's the details from my latest game:
I should warn that this could be rather spoilerish to those who are just starting out in the game for the first time.
I quick saved just before the exit of the first Irenicus dungeon and had then exited to have the first linear dialog encounter with that said villain. During this exchange with the Cowled Wizards, Imoen, illogically belying her 16 or 17 odd intelligence, opens her trap and gets involved in the fight by pitifully attempting to magic missile Irenicus twice. This of course results in her being taken away by the Cowled Wizards and seperated from the party which is rather inconvenient for such an early period in the game. So I attempted to find a creative solution to this problem by saving, reloading the quicksave and using any last magic missiles left in Imoen's memorized spells on the encounter with the locked up Doppleganger. But alas no! How this idea was all in vain. The game's linear and forced early story line means that regardless of what she has memorised, she still manages to cast two magic missile spells out of nowhere. (I'm thinking her belt???) and so there is no other way to prevent her getting taken away, which I think isn't great roleplaying.
She is only half a mage, so casting spells at will as in third edition rules for sorcerors is out of the question. This situation has taken my irritability with Imoen to new heights unfortunately - I shan't be taking her on in the party if I can help it.
Its nothing against her personally of course as she is a wonderful character. But if she's going to keep secret hidden abilities away from my usage as party leader, then she'll have no place in my party.
So I'll invite everyone to tell their own annoying or entertaining plotholes as well, as I recall them being quite a factor in Bg2 last time around....