It's a known issue, some games don't react well to being patched. That can be as simple as a small visual bug (Fullmetal Alchemist: Stray Rondo) or as crippling as really bad game slowdowns (Boktai 2, DQM: Caravan Heart). It also sometimes can be a specific cheat causing issues. I'd highly recommend testing your patched ROMs with an emulator on PC after building them (leave GBAATM open in case you want/need to make changes). So, in summary, use a GBA emulator on PC to try out your patches before packing the game into a CIA file, and test each individual cheat as best you can.