The IE combat scripting that governed the AI was abused badly by gameplay programmers in some instances of BGII/ToB, especially in the latter parts. It was common for AI casters to repeatedly activate contingencies/chain contingencies/spell triggers that contained illegal amounts of illegal spells. Often they would trigger even when timestopped! Not to mention the spell/innate ability machineguns that some NPCs were (read: Draconis). Abuse, cheese, engine/ruleset shortcomings and overall imbalance made the final battles a mess...
But the worst design decision ever was probably when LA decided to strip the superb iMuse music system from TIE Fighter Collector's ED in favor of static digital audio tracks. Yep, that made me cry.