The nuclear waste breached its containment vessels, pooled together, and went critical shortly before the building was unsealed by the arcaeologists.
This might require some mass stupidity on part of the building's engineers, but if the nuclear waste did manage to corrode the containment vessels, leak to the floor, and then find a suitable neutron moderator like water and/or graphite, then the waste material could conievably attain criticality and sustain a low-level chain reaction, at least for a while. No explosions, but substantial amount of neutrons, gamma rays, X-rays, beta rays and alpha particles could be released. Enough to kill a 300-400 lb. pony in less than a day?
Maybe. I'm not an engineer. — Pyre Vulpimorph
- And the need for the mass stupidity can be easily averted. As someone on Fimfiction pointed out, what if the first expedition to enter the storage facility found a bunch of intact storage casks, and smashed them open to get at the treasure they were sure was inside?
- It's mentioned in the story that other civilizations had found the building, sealed it back up, and added their own translation of the warning to the walls, somewhere between 26,000 years to the earliest of 5000 years old. As a result, something could have gone inside and messed with whatever containers the waste was being stored in, then sealed the tunnel back up.
- In the Fimfiction comments, Word of God says that a possible explanation is that ponies are affected differently than humans are.