If you have used a Mac to transfer ROMs to Retropie via Samba (SMB), note that it will create a metadata file prefixed with "._" for each file you copy. These show up first alphabetically in Retropie and trying to play them results in them failing to load.
They can be deleted by enabling SSH on the Retropie and removing them via the command line. Likewise, enabling SSH and copying them, using SFTP should keep the ._ files from appearing in the first place.
