My wife and I have a fairly large base and with workbenches etc set around the place. We hadn't had a spawn of any kind inside for probably 50 in game days or more. Then one day I heard noises and found a skelly attacking some off our stuff inside the "no spawn" zone.

Killed the skelly and then wandered around the base for between 5-10 minutes before I found the one little spot that wasn't covered. When I say little it was smaller than a standard floor piece. Needless to say it's covered now and no more spawns.

The point of this is to say check, double check and check again to ensure every last inch is covered.