So I've noticed these terrain pits randomly forming in my terraformed structures. Sometimes these fix themselves naturally, but generally I try to jump in the pit and fix it manually. I've also timed-out to the server multiple times when jumping into one of these terrain rifts to fix them. I can generally find at least one at any given time, on my castle or sphinx, after logging in.
Screenshots are dark, it happened to be night when I thought to take some pictures. I outlined the pits in yellow though. What is difficult to see in the screenshots is outlined in the picture above. The pits extend much deeper than the outlying terrain, and end at a single point, rather than 2 to 4 points like something player made.