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The Amathea fight crash has been resolved, and you can fix by downloading the lastest version. Thank you for finding the second crash. I will look into it ASAP!

Got the latest patch and confirmed that this crash is from shooting a door in the Metroid section when an enemy tries to go over it.  Same crash as above.

I also got an out of bounds clip, that I was unable to get back in bounds from.  It was in the Kid Icarus part of the maze, when trying to get the key, if you jump when crouching, you can sometimes clip out of bounds.

I had a shortcut room not work in the Zelda section, it was the shortcut room to the boss chamber from the start to the boss room in the far NW dungeon (Minotaur boss).  The shortcut room works going the other way (from the boss room to the exit), but it would not let me exit on the boss room side when going from the entrance.

Finally, if you defeat the Minotaur boss, then get the Biforce without picking up the heart, the heart is lost.  It's not present if you go back to the boss's chamber and it doesn't appear like it's possible to get it again.

Otherwise the latest patch works wonderfully!