Allright, after playing through I found this.
When you are in the forest fighting Team Aqua for the first time. Once you get to the end and have a double battle with the 2nd in command, If you only own 1 pokemon at the time, then it put's that 1 pokemon out twice.
(Example for me: I have toadidile so it sent out 2 lvl 17 toadidiles.) Then, when he got one of them down to 2/48 HP I tried to use a potion and it said I had no pokemon and when I went back to the battle both my pokemon were gone and There HP was both at 0. That is where one of the enemy attacked and made the game freeze. [I would love it if you could fix this.] More glitches if I find them...