The end of dungeon bug happened to me twice. First at the end of the 2nd dungeon, Bottle Grotto, and then again at the end of the 5th dungeon, Catfish's Maw. Both times, closing and relaunching the game allowed me to progress.
Other bugs I've found:
-Interacting with the Face Shrine keyhole opened the door even though I didn't have the Face Key yet. I only have one save file, so I haven't been able to test if this will happen in every playthrough, but I had just been told by the owl that there were two shrines I should check out, one to the south and one to the north. The one to the south is where you get the Face Key, but I went to the north first instead, and was able to open the Face Shrine and enter without first getting the key.
-The Armos Knight in the ancient ruins south of the Face Shrine (where you get the Face Key) can only be damaged by charging into him with the Pegasus Boots. In the original game, he could be damaged with the bow, or with a charged spin attack.
-I found myself unable to leave a cave once (Link was just pushing against the opening as if it was a wall). This was in the cave at C-2 (the right entrance) after I'd jumped off of the ledge inside (the one with the green skull). After a few moments, Link disappeared and reappeared on the ledge, and I walked down the stairs and was able to leave the cave. I haven't been able to reproduce this.
-My game crashed once while leaving the cave at L-9 (I think? I'm not 100% sure which cave it was, but it might also have been the fairy fountain at I-8... I wish I'd written it down as soon as it happened). When the crash happened, it displayed this message:
Index was outside the bounds of the array.
at System.Collections.Generic.Dictionary'2.TryInsert(TKEY key, TValue value, InsertionBehavior behavior)
at ProjectZ.InGame.SaveLoad,SaveManager.SetString(String key, String value)
at ProjectZ.InGame.GameObjects.NPCs.ObjMarin.StartSinging()
at ProjectZ.InGame.GameObjects.NPCs.ObjMarin.Activate()
at ProjectZ.InGame.GameObjects.NPCs.ObjMarin.Init()
at ProjectZ.InGame.GameObjects.NPCs.ObjMarin.Init()
at ProjectZ.InGame.Map.ObjectManager.LoadObjects()
at
ProjectZ.InGame.GameSystems.MapTransitionSystem.ThreadLoading(String mapFileName)
EDIT: I've reached Eagle Tower, and I have a few more bugs to report.
-I was able to lift up the skeletal remains of the flying rooster in the cave below the rooster statue without playing the song to revive him. I found myself holding the flying rooster, like normal. But he wouldn't follow me out of the cave until I played the frog's song.
-Sometimes, you can't pick up the flying rooster from certain angles. This has led to me getting softlocked at the end of narrow corridors, unable to lift the bird, but unable to walk past it either. Exiting to the title screen and reloading the game resolves this.