On both The Division and The Division 2, the SnowDrop engine can end up spawning enemies inside of walls and over/under the playable area.
What is the best way to deal with this? If I'm on a mission, how can I complete it?
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On occasion this has happened to me.
In some cases, enemies are stagnant until the existing enemies are cleared from whatever arena you're fighting in. Clear out the zone and the some enemies standing off to the side will become active combatants.
Likewise, these enemies may be on positions that actually are navigable but you need to find a way to reach them. Keep an eye out for scaffolding to climb, unlocked doors, or rappels to ascend or descend to bring yourself to their position.
It doesn't sound like these enemies are waiting for you to finish fighting, though. Instead, try using explosives or fire to eliminate them from otherwise unreachable positions. I've found that the drone from The Division 2 can be commanded to attack unreachable enemies with decent success.
When all else fails, it is sometimes necessary to kill your character/restart the mission to get enemies to spawn in navigable positions. If it happens regularly for you, try recording it and submitting a ticket to Ubisoft.