Well, the map loading bug is still in the game, if you walk on the path to the CRT Building (but it works on the way back.)
Shuffle bug is still in, once again only for Squirtle's Mission.
And the first new game breaking bug is an audio file failing to load in the diglett battle. "audio/bgm/Megaman%208%20%5BPSX%5D%20music%20boss%20intro.ogg"
My guess is the %20, %5B, and %5D (which represent a space, [, and ], respectively.)
This one is funny, if you "talk" to a pokeball from the side, It turns into a bed. And talking to the bed from the front turns it into a pokeball and from the top turns it into a Snow-Parichisu. The bed turns back into a bed when you stop talking to it.
I think the game crashes if I shift (dash) up to a doorway and interact with it.
At least pokeballs stay gone when you pick them up.