the music still playing after you load the state seems to have an interesting effect in Actraiser 1, reloaded a save state at the first boss right before the music switch for the boss fight and the boss music never started and the boss AI never went into action, just stood in place while i walked over and finished him off, can't say for sure this doesn't happen in regular emulator savestates but thought it was funny
Emulators generates a full save state of everything, including APU, flashcarts savestates don't and I think that never will happen.
Some games can crash because, there's a file (savestate_fixes.yml) in the package with some fixes for games with audio issues, basically the game stores the state of the APU ($214x) somewhere in the memory and it needs to be updated right after the load/save state.
RedGuy made that fix list, but he won't work on this savestate stuff anymore. I'll try to fix some games but I'm not a expert debugging them...