As posted by sbm12, if it's all on UA flight numbers then their rules apply.
With at least one segment already in First there should have been no problem.
What seems to be happening with the IATA 302 and MSC is that check in agents are relying on there screens rather than the rule book as the correct allowance is supposed to be incorporated into the eticket; from other anecdotes, it appear UA have not correctly set up their allowances with APTCO.
If "computer says no" then you have a problem.