Generally this is not a problem - Here is the typical scenario -
MAMEdevs discover PCB for GameY and extract the Data from ROMS A, B, and C, and it gets added in MAME 0.56.
Later, they find out the ROM D and E are also required (but were on a different part of the PCB, so for MAME 0.75, GameY uses all five ROMS.
GameY will work in either Build with the 0.75 Roms, but the 0.56 Roms won't work in 0.75.
There are exceptions - often the MAME team will rename roms from the set.
www.clrmame.com will usually fix this. Also, sometimes roms will move from one set to the next. This won't matter as MAME will search all the sets, but Clrmame will clean this up too, if needed.