Hi there
@Jlavigne - try deleting the shelter in the habitat, and call the keeper again. It's a known issue and it might fix it. Basically, poo gets stuck under the shelter and the keepers can't scoop it up.
Also, a mistake I made was not putting water filters next to all the keeper huts, and next to habitats where your animals drink from pools or rivers - this keeps the water they drink clean.
I hope this helps. Good luck!