I cannot identify what is digging those holes. This could be wildlife or a feral domestic animal - It looks as though there are claw (?) marks on the pipe, but beyond that there it's impossible to say beyond guessing. I recommend borrowing or buying a trail camera. 
Prevention of additional excavation will likely be assisted by laying an undiggable surface apron of welded wire fence  or hardware cloth. Probably (?) 18-24" will block the behavior, but it's hard to say without knowing what critter you're having to deter. Alternatively, hardscaping that area could be another thing to consider, but also a decision best-guided by further ID information.