I would try moving (or deleting) your gamelist.xml and roms for the 2600 and see if that helps.
The gamelist.xml should be in .emulationstation/atari2600 (or atari2600-libretro if you used the retroarch emulator instead).
So I would:
1. Quit Emulation Station
2. Move the gamelist.xml somewhere else so it won’t be read
3. Move your 2600 roms somewhere else
4. Restart Emulation Station, verify that the 2600 doesn’t show up anymore, and then see if the issue goes away