Armadillos, moles, rats, opossums, mice, and skunks all can likely be the culprits of making holes in the dirt at night time. You can check out the size of the hole to guess what may be digging in your yard.
It's proven that Armadillos, Opossums, Groundhogs, Squirrels, Raccoons and other mammals like Rats are night active, but it may surprise many that Skunks, Hamsters and Margays belong to this group.