I just assumed in those cases it either wasn't finished when they were building it or collapses happened

This can happen but its a rare occurrence....

It happens. Even with Burial Chambers--some of them have no cores. Some have like upwards of 16.

Hooray for RNG!

Sadly there's little to alert you to this fact before plowing down the time for clearing it... The variance as such isn't a bad thing, but the lack of communication from the game is.

OTOH Valheim "dungeon generation" could be better on the whole. The large number of dead end paths that end with a door or stairs and then just abruptly stop is another pet peeve of mine. Like anyone would bother building like that.