EDITED -- Still unable to complete.
A5 new information: If Link pushes the water switches partway, in a manner that causes the "switch movement" animation to pause halfway through the animation (i.e. starting to push the switch, but not completing it, not pushing the switch long enough), then there's a 50% chance that the graphical glitch occurs where the lever is set based on the direction Link is looking (left or right only so far. Haven't observed this glitch when looking up or down.).
A14. Fairies are still getting stuck on terrain.
A41. Cave of Adventure: defeating the Stalfos doesn't get rid of the Boss icon on the map, as it would if any other boss is defeated.
[1]A42. Underwater Prison: scribbles on the wall might need to be proofread. Unless the point was for the text to be rambling?
[1]A43. Soldier Tombs: returning to the room where access is granted to the basement (after lighting the four torches), sometimes the central statue isn't moved.
[1] Reloading by exiting the dungeon or using the Magic Mirror solves this, though.
[2]A44. Desert Palace: Incorrect tiles in some of the rooms.
[1] [2] [3] [4] [5] [6] [7] [8]A45. Darkworld, area outside of Swamp Ruins: when going underwater, it looks like one graphic layer is placed on top of Link's sprite in some parts of the room.
[1]A46. Is Mining Town supposed to keep the day-night cycle like the rest of the outdoors areas (like Heimgartner Manor)? Because I entered the Mining Town area at night, and the location is lit up as if it's daytime.
A47. Mining Town:
key didn't spawn. Unable to complete, out of keys. Might be similar situation to A29, where the slimes aren't killed in a triggerable area to have the key drop down?
[1]A48. Starting with BOSS name, I load into Mining Town but then am stuck. Similar as in issue A37.
A49.
Mining Town: I've only been able to find 3 keys, and 4 locks. One of the locked doors can be circumvented, which leads me to believe there is softlock potential here. Solved. Sometimes the key fails to load. Resetting the game solves it, it seems.
A50. Mining Town: more tiling issues.
[1]A51. Mining Town: warp tile not functional unless the dungeon is reloaded.
[1]A52. Derelict Mine: tiling issue hiding a Weight Crystal switch.
[1]A53. Derelict Mine: I keep getting stuck on some of the doorways. Always need to Magic Mirror or Save&Quit to get out of it.
A54. Derelict Mine: Appear to be stuck here. Unable to get the Weight Crystal to the right side of the room. Unless there's something I'm missing?
[1] From what I've been able to tell, saving after flipping the switch, then reloading, will cause the room to keep loading the enemy slimes on the lower level, making it impossible to move the Weight Crystal to the right side of the room.