Anticlimax Boss: The Big Bads of both games are relatively easy to handle because of level design. The first game's big bad becomes much more climatic if you defeat him properly with the quest item Wand of Silvias.
In the first game, applied literally with the Giant Spiders. You meet with them in a part of the dungeon where you're unable to backtrack and must find the way out, while too low-level to have any spell that durably neutralize their venom, and thus dependant on the few counterpoison potions you can find.
In both games, thri-kreen (mantis warriors). They're incredibly fast, hard to kill, and have a paralyzing bite that makes it pretty sure one of your meat shields will be incapacitated before having even a chance to strike. So tough they are, fighting them one-by-one is actually a less favorable option than facing a swarm of them — then at least you can spam offensive spells more efficiently.
The Stoneskin spell in EotB1. Once a scroll with this spell is found and a magic-user is of high level enough to cast it, the whole party can be basically made invulnerable to physical attacks. Only monsters that can do magical attacks still stand a chance. This is because the spell has no set duration, but will only fade once a character has suffered a certain number of blows. Hence the magic-user can cast the spell, then the whole party can rest so Stoneskin is memorized again, and so on until every member is protected. The protection can be quickly soaked up in a fight for the front-rank Meat Shields, but it can just be cast again as soon as dispelled... and for the Squishy Wizard or The Medic behind their lines, one casting may last very long since they are rarely hit. Not surprisingly, Stoneskincompletely disappeared in EotB2, even for a party coming from the previous game, an exception to the Old Save Bonus.
In The Legend of Darkmoon, though they are both five-level spells, the combo "Wall of Force + Cone of Cold" can be quite effective. To clarify: a Wall of Force stops all the monsters and every attack spells — except Cone of Cold which can be used through it, and covers a wide area to boot. May be a Good Bad Bug since that shouldn't be possible by AD&D rules (unless you have very creative players).
Good Bad Bugs: The Aid spell can raise a character's hit points total above the max, but only temporarily (unless right before a fight, it's unlikely to be of much use). However, damage from a fall mucks up the calculation, and you can end up with more hit points than before for a while, even above your maximum, including after the expiration of the Aid spell.
Fanon Discontunuity: The third game is generally considered the weakest of ye trilogy, and as such many would rather pretend it ended with the second one.
Porting Disaster: Apparently, a Game Boy Advance cartridge can't hold as much information as a DOS game. Who knew? Anyways, the GBA remake of the first game left out all but the four basic character classes and much of the gameplay. Instead of the first-person combat of the original, it uses an isometric system like the gold box games.