Hm, yeah--if you're following the order from top to bottom, Ex:
Bun
Meat
Onion
Bun
-> Bun, then meat, then onion, then bun
Then everything should work and register fine. I haven't been able to recreate the issue you mentioned, so unless further reports with documented evidence come in, I can't figure out what to fix--so sorry about that!
Luckily though, skipping minigames will not lock you out of progressing the story!