Atlas Passives in Factory Map not working

I have Exotic Goods & Great Migration.

Both the Invader and Beasts seem to not spawn sometimes when running Factory Map (T3).

I have done the map multiple times to see if it was a coincidence, but after testing, I can confirm it is not.

Here is a screenshot where I have 21/28 Beasts and can't find the remaining 7, the Invaders didn't spawn either.
https://i.imgur.com/rQL20wG.jpg

There was a Harvest in this map, however the issue seems to be regardless of Harvest.