I have and iron farm and i have experience it every time iam not around the farm, the zombie in the system (has a name tag) disappears every time HE IS STILL THERE but he is invisible and this can affect that villagers doesnt get scared.

As you can see there is nothing where the zombie should be but he can deal damage and also he makes voices (right corcner) this scenario can cause villagers doesnt get scared only after i reset them.

The zombie appears if i leave the game and rejoin.