I'm good at breaking things, usually without meaning to, so here's what I found so far.
1. The player's health can go NaN. I hadn't fought anything prior to checking the chests in the village when I found the trap, so I used skills and potions to avoid dying. When I ran out of mp, I almost used my mp potion, then backed out, hit skills again (wasn't sure what TP did) and somehow made a skill target Link. Upon it activating, my health went NaN. Basically makes you unkillable for the rest of the game.
2. The player can pass through most walls close to a door on the outside of a building, usually all the way to the actual doorway. The one exception is the large house on the hill near the beach, which you can enter from the right and get stuck permanently in the mountain if you go too far left.
3. Not entirely sure what triggered this one, but the trap chest by the cave can slide after opening. This was my second run, and I tried opening just the non-trapped chest, but it opened both, starting with the trap. After the fight, the trap chest slid all the way to the right while I got the text for it being empty and getting the contents of the other chest.
Not really glitches, but I also noticed that the skill attack for the octoroks doesn't do damage, and trap enemies both lack a non-skill attack and xp after beating them. All in all, it's pretty good so far.