Welcome to Continental where the COmputer is always right.

The web system is probably more thorough at finding the lowest fare. It's possible the agent quoted the upgrade for AMS-MCO, whereas the computer found the cheapest possible combination of upgrades for AMS-EWR + EWR-MCO.

Also the date of ticketing may come into play. The system is supposed to find the lowest possible F/BF fare at time of purchase and offer it to you. It's possible that if you ticketed on different dates, there were different fares filed.