Q.Something Is Producing Many Small, Thumbnail Size Dirt Clods Overnight. Also Occasional Finger Size Holes That Seem To Lead Nowhe
re. I am very familiar with moles and gophers. Clods are scattered over a dirt area approx 5′ in diameter. No loose dirt, only formed small clods. Maybe 10-15 each night. Only one plant close-by with no apparent damage yet, though maybe roots. Some large rocks that will be difficult to move. Can send foto if someone wants to see dirt clods. Been here 30+ years. Never seen this. No ground cover, grass or other cover in the area.

Certified GKH Gardening Expert
It could be earthworms or other insects. Earthworms tunnel through the dirt, ingesting the soil for organic matter. They leave castings, which dry into small lumps of dirt. Here is more:
https://www.gardeningknowhow.com/composting/vermicomposting/benefits-of-garden-worms.htm