Homebrew I need help with my Roms

[Cactuar]

I am learning how to use Clrmamepro. Sometimes when I scan my NDS rom collection Clrmamepro will find discrepancies with a Rom archive. Sometimes It's a CRC error/mismatch or within the .zip file there will be an extra folder that is unneeded. I try to extract the file and rezip it but then I get CRC errors. I believe The Roms I have are the proper scene releases. Can anyone shed some light for me please?