Occasionally, they can get stuck in walls/floors, or the marker can be incorrect, it can also be pointing to the spawn point of a patrol. Push come to shove you send in a gm request for help. They can pop enemies out of walls or complete missions, but if it's happening repeatedly, they you might want to also report it.
If you've cleared all the floors, look at your map and there should be a red arrow(s) indicating the last mob. Out of curiosity, which mission/contact is this?
Edit: Most warehouses are generally a single level, though some will have freight elevators to take you to another level, like the ones in Pocket D and there a few that open freight elevator doors with stacks of boxes that you climb to get to another level.