Hmm, saving at the wrong time.
I recently played through Fire Emblem Three Houses, on one of the routes, the game tells you 'your choice will drastically effect the story'. I reset the game real quick, made a copy of the file, and continued playing. Then just a few chapters later, I accidently overwrote the pre-decision file anyway! Meaning I'll have to play through the first half of the game again to see that other route. The game is great, but that's a lot of time I could of saved myself.
I remember Wario Land 4 had autosave. Once you beat a boss, the EXACT moment you beat them, you better hope you beat them with all treasure intact. Because if you don't, you just missed the perfect ending and they are gone for the rest of the playthrough. A lot of killing yourself on the bosses, for some reason you can't quit or restart in boss stages in Wario Land 4, that was always really weird and annoying.