I understand that when using the import content option of RetroArch, only the ROMs whose CRC32 matches a given database (I’ll assume redump.org) will be automatically added. For most platforms it works as expected, but games in ISO format are never accepted even if they are perfect dump (example PS2 games in BIN/CUE are fine, but not ISO). Is this a bug?
For large (usually optical media-based) ROMs, it uses magic numbers / serials when possible but sometimes IIRC it uses a checksum of the cue file. That might be what’s happening here.
I would recommend just using the manual scan in that case.