For me one of the biggest issues is that once a certain amount of animals in one habitat is reached, one keeper just isn't enough to keep all of them fed.
I have like 15 pronghorns and 8 bisons in one enclosure and almost every time some of my pronghorns are starving before the keeper refills their stuff.
Also I have multiple troughs in the habitat, only one gets filled with food for the pronghorns and one for the bisons, but after all the food is gone from the pronghorns one, some pronghorns are still hungry! But keeper doesn't refill until after they're starving again. Urgh... it is annoying as hell