I always go straight to the training mode when playing fighting games, and when I tried to access it, I got this error message: 

___________________________________________
############################################################################################
ERROR in
action number 1
of  Step Event0
for object oMainMenuIcons:
Variable <unknown_object>.buttonMenuConfirm(100023, -2147483648) not set before reading it.
at gml_Object_oMainMenuIcons_Step_0
############################################################################################
gml_Object_oMainMenuIcons_Step_0 (line -1)

Also, I couldn't do anything in the options menu, it was like the game simple froze, and I couldn't move my character in versus mode (I play alone, I was just testing to see if it worked)

I rarely play this game, but I've been following this game's development for over a year, and I'm a dev myself, so I hope this isn't too demotivating for your guys, I know what it feels like when you push an update and stuff just falls apart. 

Just replicated the bug you described. Happens if you immediately go to training mode after loading into the game. I think I know the root cause, though, so I should be able to get a fix out quickly (controllers themselves don't have anything to do with it.)

The other two issues you describe actually seem to be related to the first. If you replicate the first bug, you will not be able to move on the options screen or control your character.