I had it happen in some places before the caves were in testing.

For me the ground would pop out of shape from how I leveled it but one hit with the hoe set it back. It was odd though. At first it would pop up or down then it seemed to settle down a bit and happen less often only dropping down.

Only one spot. But I don't normally do a lot of ground altering and typically work with it. In this case it was just an area on a hillside just above the back of a troll cave. Leveled it off to accommodate a kiln and furnace.

I also have one area that is glitched after trying to level it. The entrance to my main residence in our second largest village. Just a small strip of land but it is very frustrating. This glitch began last year so it is not being caused by the latest game upgrade.
https://steamcommunity.com/sharedfiles/filedetails/?id=2687397099
https://steamcommunity.com/sharedfiles/filedetails/?id=2687398370
https://steamcommunity.com/sharedfiles/filedetails/?id=2687398881

I've the same problem in one of my bases, single/local world: I flattened the terrain but, sometimes (didn't find the "triggering condition") it opens 1 m deep "hole" and I even can walk into it (so the physics is "preserved", the engine knows it as an hole, not flat terrain).
Only things I noticed are (1) items remained suspended over the hole seems not suffering the loss of support, not breaking/decaying, and (2) if I leave and get back (or even just after some time I'm there) the terrain gets back flat as usual.

First time I saw that effect I thought it was me, to make a mistake, maybe flattening/digging at night, when the 3D perspective is weak, so I re-flattened (raised) the terrain up... only to find a little "hill" later. :D
Since that moment I just ignored it, thinking it was a terrain-map's glitch.
I can confirm the problem lasts far before the last patch/update.

I have one location that changes when I terraform around it.
Try leaving the area and coming back. Does it revert to how you want it?

It was reported during caves beta... I guess they are working on it??