The problem with that is, judging by our own behavior, an unknown ancient structure makes humans investigate it, try to dig it up, etc. Placing a marker isn't the problem, the hard part is communicating "nothing interesting, only death here, do not enter" in a way that someone in 10.000 years will heed the warning.
The solution is to build them everywhere and put the bad stuff in one of them. If you build enough then the chances of them excavating the one with nuclear waste is pretty low.