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I fixed the problem. I used the final version of the patch and it worked. I guess I was using the old one before and it didn't work.
So far I beat the first gym boss, so far it's clean no bugs/glitches.
I successfully patched the file but when I extract the file to my android the game is the original emerald and not expert emerald.
What I am doing wrong the the game ends up not being expert emerald though I patched it.