I’m going to take a stab and say they were improperly tagged in your collection. I had a jakey looking nes collection with a few hacked roms that got named to weird things. I “lost” some of those games, but found them under wrong names and boxart images that simply didn’t match the rom. Such is the nature of fuzzy logic.
You can go through your haystack until you find your needle, or you can get into the GoodTools programs (allgoodthings.us) and get your roms properly named to conventional standards, then rescrape your collection. It’s a long and tedious process depending on how many roms you have to manage. Don’t feel alone in that, though. I’m still not done cleaning mine up, lol.
Good luck, let us know if that’s the issue.