Both of them get saved under GarrysMod\garrysmod\data\zmlab\
- MAPNAME_MethNPCs.txt
- MAPNAME_MethDropOff.txt
You can remove them which removes them from the Map.
Easier way to remove them individually would be to remove the Entity with the Remover ToolGun and resave them using !savezmlab in the Chat. This will override both files for the Map.