That should be you mixing MAME roms with softlist folders. I.e. there's a 32x.7z/32x.zip file (MAME ROM) and a 32x folder containing all 32x cartridges. Given romsets could also be uncompressed and into folders, that's considered a duplicate conflict.
I for example have 3 different folders: MAME\romset MAME\softlist MAME\chd
I also drag all xml files from hash folder to ClrMAME and batch scan instead of ClrMAME loading the softlists for me.