If you use something like
www.mameui.info you can check the roms within the program (it's called audit), so just audit the game you are running into problems with and will report if any files are missing or have the incorrect crc
The biggest problem with mame is that with every update some roms also get new dumps so not all the old roms will still work
Don't get me wrong I still think mame is great it's just it is a pain to update the roms with every update, but this is part of it improving with every update, they also use the best dumps possible at the time.
P.S. chd compression is another thing that is changed, mame should come with tools to handle/update those though, just read through everything first