Expeditions don't get consumed on the map. After you clear a normal dungeon, the square it spawned on and ones near to it are cleared and no new dungeons will spawn there. Because it's theoretically possible to clear out enough of the map that no new dungeons can spawn, you'll need a way to have permanently present dungeons, which is what the Expeditions are. It's also why the Expeditions are located in the farthest corners of the map.
I actually did this on my last playthrough. I wanted to clear out the starting area before tackling the ratling fort and ran into that situation as I was getting down to fewer and fewer uncleared tiles.
I think it might be interesting to have places you've already cleared get 'uncleared' by invading enemies. Not a regular occurrence, but perhaps a random chance if you don't clear an Elite+ dungeon or something? Or invasions spawning from those Expedition squares. Probably a bit too much to add at this point though.