I don't think I would repair it. Getting a good patch would require further digging in to the concrete. I would probably recommend that the owner reject the beam or accept it and get a credit from the contractor.
If it's an interior box beam leave it alone. If it's the fascia patch it - otherwise some passerby (or future bridge inspector)will think the bridge has a problem. You could drill in some 3/8" hooks to hold the patch.
The hooks won't hurt the concrete. You won't need much embedment for a 3/8" hook. The idea is to have a mechanical bond to hold the patch matrial. Corners can be tough to fix.