This error message comes up in games that use 128k Flash chips. The default setting in VisualBoy Advance is to emulate a 64k Flash chip. To fix this, go to Options > Emulator > Save Type, and select "Flash 128k." Be sure to delete any .SAV files for the game before doing this. Otherwise it will continue trying to use the corrupted save file.
This error would never occur on a real Game Boy unless the cartridge is a counterfeit copy.