the only foolproof-ish way i've found to avoid that is base layout and rush tactics instead of camping. certain facilities have holes to the sewer Z-level that enemies can easily wander into. Extractor is the worst for this, but Plantation also has a few holes and most wrecked buildings or rubble are also problematic. i try to place extractors as far away from enemy spawns in hangar/elevator as possible to avoid units falling into the hole.
you can use Dogs and other units with a motion tracker (Aye-Phone) or Sense (ex. cat, bugeye) to scout for enemies that aren't on the main Z-level. this allows you to quickly clear map tiles without descending.
the green hellerium sludge in the sewers is flammable and can be ignited with a simple molotov, however i've found this isn't very effective at area denial because the fire spreads too slowly.
enemies with depleted Morale will panick just like your units, and panicked units count as surrendered/unconscious for purposes of ending the mission. the only common enemies that are immune to this are animals and robots (ie dogs and drones), so make sure to kill those enemies first. it won't matter if a mook-tier enemy gets lost in the sewers if they're panicking and surrendered anyway, but a dog or drone will force you to go down there after it.
otherwise, simply kill the enemies fast so they don't have time to wander off and get lost.
