It's from an old set and easy enough to fix if you know what to look out for though still very annoying
Can't say I have seen any PSX or PS2 games with the same issue though, but this is a well known issue with the Saturn set uploaded to the main site
PSX is only a pain for those ecm file and the ecm and ape combos that require converting fully ecm to bin and ecm+ape ones not only need converting to bin+bin or bin+wav but also need to be converted back to a single bin+cue