My head cannon was always that someone figured a way to trade with the surface at some point, then covered their tracks.

Someone dropped something down an air vent to hide it, maintenance go to figure out why fan 56 is on the Fritz again and find something.

Over 100s of years there’s ways to explain and then have people forget how things ended up how they are.

How some of the skeletons stay undisturbed is a mystery though.