Jaded and I have both seen this on our generated maps. What we did was to edit prefabs.xml on the server; find all the Canyon_Cave entries that had negative Y values; and change them to 1. Save, restart the server. Clients had to re-download the map, but nothing was lost.
We also each provided the prefabs.xml file in discord with instructions where to copy it. That was enough to avoid a full map re-download.
The result will be that the adjusted prefabs will appear a few blocks above ground level with sheer cliffs surrounding them, though not very high (worst case on both our servers: 7 blocks); but at least your users won't fall through the map, and your server won't crash when somebody gets a trader quest on that POI and the bottom of the prefab comes crashing out of the sky.
Before:
<decoration type="model" name="xcostum_Canyon_Cave(by_War3zuk)" position="-3295,-6,349" rotation="0" />
After:
<decoration type="model" name="xcostum_Canyon_Cave(by_War3zuk)" position="-3295,1,349" rotation="0" />
Alternatively you can simply delete those lines; I believe those prefabs will simply no longer be there, leaving empty terrain. (In case that's not clear: I don't mean there will be a void in the map. It'll just be like there was never a factory there.)
YMMV. We've done this on exactly two maps, each on a different server, so it's not like we have a huge statistical sample to work from. None of the other prefabs had this problem, just that one, and not all instances of it.
OTOH, out of two maps we've generated, both of them had the problem of below-zero instances of this prefab, and at least one server crash as a result. It does seem like a bug that wants fixed.
[edit] To be clear, my post and GneX's don't contradict each other, they're solutions for different places in the process. His will make sure any newly-generated maps don't have this problem in the first place. Mine is a post-fix; if you have an existing map you don't want to throw away and start over, you can edit the file and fix it without losing any existing game info. The worst effect, as far as we can tell, is to force the clients to re-download the map itself.