OP quote: I said something like "Wait, don't forget about us" to her to let her know that we still needed to go.

I think this is where the OP set things off. The OP says "something like", which more than likely was a bit more curt than what was posted.

Since the OP was standing BEHIND the wheelchair occupant, that the Operations Agent already figured out was not supposed to be on this particular flight, this wasn't the proper place to be standing. They should have been right by the podium where the Operations Agent collects the boarding passes; like the OP and their son were the next to board.

Agreed that the Operations Agent shouldn't be "condescending". The OP shouldn't either.

Move along...nothing to see here.