The way I do it is use .cue files and remove .bin from es_systems.cfg
because sometimes you will find bin files with multiple tracks, like 30 or so for one game which will show in ES.
I delete the .cue/.ccd/.mds (if they are with iso,img,mdf etc as they arent required for those formats)
only the .bin files require the .cue as mentioned above.
That’s what I did anyway to resolve the same issue.