Any time I kill the boss of Sigma 1 (the section after the space and sand bosses) with a level 3 charge consistently turns the game into a powerpoint presentation where the stage slowly moves upwards.
Edit: It's now happening with a level 2 charge. I have no idea what to do about this. It just freezes for 5 seconds on the final hit before resuming every 3, the music keeps playing normally, the stage moves up until its off the screen while the explosion plays and the screen gets progressively whiter (presumably a normal part of the explosion).
Side note: this happened on both the 1.00.1 and 1.00.3