New game, no mods, no cc, just store content, after the full moon the zombies did not go away. I did a resetsim * and it cleared them out, but a few sim hours after another spawned from the ground. This time I made sure to lock all gates around the garden so it doesn't look like a total zombie apocolyps but I thought they were just suppose to hang around for a full moon.
Interestingly enough, in Sunlight Tides (an old save) they spawn and disappear like normal on a full moon, the town I am having issue issues in is Moonlight Falls.
Edit to add it is fairly entertaining for now, but I am hoping its something that can be fixed ;)