It was probably not rusted when the filler was applied, but rusted right afterwards and continued on, over a period of time.

Production style work usually entails applying filler to clean bare metal.....the filler gets quite hot as it cures, then cools off.
Beginning with that first temperature change, immediately the stage is set for condensation to form. The slightest chip or
failure anywhere in the topcoat allows moisture to contact the filler which absorbs it like a sponge. If the vehicle
is ever wet sanded and cut through to filler happens anywhere, water touches the filler....then later on, the metal will be rusted underneath.
(DAMHIK).

These days I really prefer to apply filler to areas that have been stripped, sprayed with 2-3 coats of epoxy, and then the filler applied during the recoat period.
The metal is protected against moisture 1000% better than the other method, and the epoxy Helps "glue" the filler in place.
The bond is much stronger than filler's bond to bare metal alone. Production shops seldom do it this way because the first coat of epoxy
does not contribute anything to the appearance of the vehicle, and is therefore considered a waste.

This is why.....sometimes, "Take it to a Pro" can potentially be the wrong answer from certain perspectives.