Which emulator(s) are you seeing this with?
I see lots of entries for the same game with the PlayStation emulator, as Emulation Station is displaying all the files which make up the game (at least, all those with extensions it 'recognises', as specified in the es_systems.cfg file for that emulator)
A long while ago I watched one of the excellent RetroPie videos on YouTube from forum user @Floob in which he covers using a tool to combine the elements of a PlayStation game into a single file (Iso, or similar, if I recall correctly), which cleans up the list in ES
In the Spectrum emulator I generally see a couple of entries if I've unpacked an archive file and left both the archive and the original in the Roms directory