I was just playing this today and the controller worked great, but now when i played a bit later suddenly it started glitching out. The controller i'm using is a Nacon Wired Compact Controller which still works fine.
The (X) button, which is bound to the Jump-action is also suddenly reading the Pause-action
The (Square) button, which is bound to the Run-action is also suddenly reading the Reserve-action
and the (Pause) button goes to the Quit_Game-menu as opposed to the Pause-menu.
When i tested rebinding, i noticed that the controller seemed to read the keyboard actions. I tried unplugging my keyboard, but it seems like the game reads the actions anyway, without the keyboard. I don't know how to fix this, other than maybe starting a new file or just using the keyboard only, but either way i'll post this as a Bug Report.