Take the freeze (atari) game (mame 0.123)
It has a main game (freezeat), and 6 clones.
In merge mode, you should have only freezeat with all clones roms included.
But look in the clones:
freezea2
- fish_gr0.07-00 06559831
freezea3
- fish_gr0.07-00 3aa389d8
freezea5
- fish_gr0.07-00 7ba4cb0b
freezea6
- fish_gr0.07-00 3fca32a3
Crazy
Of course you can't have all fish_gr0.07-00 in freezeat.zip.
RomCenter detects the problem and leave these roms in their clones file, even in merge mode.
After the fix in merge mode, you will have
freezeat.zip
- all mergeable roms
freezea2.zip
- fish_gr0.07-00 06559831
freezea3.zip
- fish_gr0.07-00 3aa389d8
freezea5.zip
- fish_gr0.07-00 7ba4cb0b
freezea6.zip
- fish_gr0.07-00 3fca32a3
The rom filename is the correct one, and mame will always find them because they are in a 'correct' clone zip.