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this may be one thing or a couple of overlapping things, not sure. it's fairly infrequent, at least in my experience. doesn't seem to be dependant on any particular version: i've noticed this across multiple builds, most recently 220.127.116.11 while editing the beginning fortress.
the first part is that sometimes you'll cut off a chunk of an existing design in build mode, that chunk will drop off as you'd expect, only the game marks the dropped pieces as destroyed rather than removed, leaving ghosts for repair systems to try and fix. not the blocks that you specifically deleted, only the ones that dropped away.
you can manually delete the ghost blocks, but the whole point of cutting off that large chunk was to save time, and deleting a lot of ghost blocks is more annoying than deleting normal ones.
the second part is that, because it thinks they're destroyed rather than deleted, repair systems will try to restore those blocks, but there's no connection to the main body, so the repaired pieces will hang there in coyote time, for anywhere from a few seconds to a minute or so before finally realizes it's not attached and falls off. it usually seems to properly clear the ghosts when this happens, but I'm pretty sure I've seen it generate ghosts again.
and, of course, if it's treating those blocks as having been combat damage rather than an intentional cut (which i'm guessing it is) and you're building in campaign mode rather than the designer, i suspect that you're not getting those resources back.