I dont know which emulator you are running, but with roms like Bobble Bobble (which is a clone) it needs the parent rom (which is bubble bobble).
Then the emulator you use probably looks at its config to check where the roms are, and it is directed to the main folder, and of course the parent rom is no longer there.

You could get around this by using clrmamepro to roll the required roms into each clone (or just use parents and get rid of clones).

Non-Merged Sets means that all games, including clones, have all the data needed to run copied into their zipfiles.
Merged Sets means that there’s only one zipfile for each family, with the clones moved in with the parents.
In practice everyone uses Split Sets, which keeps parents and clones in separate zipfiles without duplicating the redundant parent data.

https://code.google.com/p/mame-rr/wiki/UsingClrmamepro