Ripped off all the brass knobs and locks tonight and sanded the door down to
240grit. Dry fitted the new antique/brass knobs and locks and have a few
holes that are going to need to be filled and sanded before new paint.
It's a wood door with a very thin metal covering on the interior and exterior
parts of the door that is painted. What is the best putty to use for this?
Bondo?

Won't need much to get this job done.

TIA!

Bondo will do the job just fine. Just apply it, sand it, and paint it.