Good Bad Bugs: It's possible to beat the game by collecting scrolls in a single dungeon roughly 18 times, due to the plot-important item in it respawning.
Level Breaking Bug: In the Temple of Agamanus (the dungeon you need to clear to get the location of The Halls of Colossus) the room which holds the item you were sent there to get requires you to swim through some trenches (unless you can use Passwall). The room has a bad habit of spawning a ghost or wraith, which levitates over the entrance, blocking you from getting in. The only possible fix (assuming you have no way of using Passwall) is to save under the enemy and reload, which only sometimes works. Otherwise you'll have to backtrack through all 3 levels of the dungeon and go find an item with Passwall.