OK, I've found three glitches but I can't be specific about the cause. Firstly, the north door as you enter Level D is supposed to be locked. I discovered this by going into Level D as early as possible (after only visiting Levels O and U). Visiting Level T would mak the door unlock itself. However, on another playthrough, repeating the exact same steps through levels O and U, it was unlocked without having to enter Level T. So normally, you'd have two spare keys after completing Level D, but you're only supposed to have one spare key (which was actually a mistake by the creator; he intended each level to have the right number of keys).
The second glitch is the east door in the first room of Level S. This one is weird and I really don't understand it. On my most recent playthrough, I completed levels O, U, T and L, getting the Handy Glove. At this point, I pressed save state and entered Level S. The east door was unlocked. I reloaded state (so Level S had not been entered at all on this playthrough) and completed levels A and N. Then, on entering Level S, I saw that the east door was now locked! This really does not make any sense at all. (The correct state is that it should be locked; this makes sense regarding the key placements in the level.)
The third glitch is also in the first room of Level S. If you leave the level via the north door, the east door is unaffected (it'll stay as it is), but the south wall will bomb itself open if it isn't already. This, I'm assuming, is similar to the Level 1 glitch of the original game - leaving Level 1 through the south door unlocks the north door, so leaving Level S through the north door "unlocks" (bombs open) the south door, or something.
A possible explanation is that the game tries to move you one room further north / south, but because it can't, it tries to re-enter the same room from the opposite door, unlocking it in the process. Once it realises you would be in the same room, it takes you to the overworld so you don't actually see yourself re-entering the room from the opposite door. It's just a theory, though.
I also found another couple of minor graphical glitches. From Ocarina destination 5 (above the Lost Hills), go through the One Way cave and go west once. The timing is tricky and I'm not even sure of the correct timing to do this, but activating one or both of the Iron Knuckle statues can make it glitch up so it looks like a Ganon's Eye (the rock's replacement) while it's moving upwards. Also, if you kill the statues at the right time (which I'm not sure about), sometimes one of the Ganon's Eyes falling from the top of the screen may change into a Wallmaster sprite (the replacement for the original game's Ghini). It'll stay that way until you leave the screen, so when it reappears at the top, it'll still be the hand.
I don't remember being able to make the original game's rocks look like Ghinis... maybe if you killed a Zora at the exact right time? No idea.
EDIT: It might be possible to discover exactly what causes the doors in question to unlock or lock themselves if the memory locations which store whether those doors are locked or not can be watched throughout the game. I'm not good with that sort of thing, but at least if it's possible, it'd give some idea of what it is that causes these changes.