Gonna start this off with ... man that sucks, sorry for ya..... I think the animal spawning is still a bit wonky, but for future reference.... this may help (or it may not.. the game is buggy)
Did your pen have any foundations inside of it??
Like Ark (pillars) certain structures do not stop the spawning of resources/animals .....
in Atlas, it seems Gateways alone will not stop the spawning of animals (Gates can also be placed outside of claims)
It seems to me that two conditions need to be met to stop the spawning
- a claim flag
- foundations
it seems that foundations WITHIN a claim flag (cant place them outside of one) have a radius to stop spawns, since we have built a 3rd structure in our gate-walls.... wilds have completely stopped spawning inside (up until that, with only 1 structure, we had 1-3 wild bulls in our gates, then 2 ... it went down to 1 bull at a given time..... now we have had 0 for 20 hours)
if you have a stretch of area in your pen without a foundation.. try placing one
Again sorry man