There are a number of things that can dig up those yards. Out here in the Wild West we can have all sorts of critters digging up the yards. Wild pigs or Javelina use their noses to dig up roots, pocket gophers dig burrows and eat roots under the ground and numerous insects dig holes to bury other insects or arachnids as food for their young. By the way ignoring these holes may lead to bushes and trees dying or by being severely damaged.
So if you are getting holes or something damaging your yard it may well be the time to call in a Pest Management Professional or Wildlife Professional.