I had to re-read this to understand, but it is NOT a bug as I understand it.
If he does 3 vaccines it should give 90460 x 1(first immunization) and 90461 x 2(subsequent immunizations). This is the way all other things in medicine are billed. Code x number of times used.
I outsource my billing but it is electronically generated in AC. I have seen this is how the bills are being generated. To my knowledge they are all being paid. What insurance company is requiring it this other way?
I would talk to the insurance company, because most billing is done this way.
