One thing that may be a possibility and no one mentioned.

It could be that the check for enemy spawns looks for an open spot. If it finds an open spot it can spawn in the enemies in a certain radius around that spot.

So the specific place they spawned my be "covered" by a bench. But they were able to spawn due to a small opening in the coverage area close by.

Just make sure all your base is fully covered/overlapped by bench radius markers without leaving even the slightest gap.

Not sure this is your issue but just something to check.