I don't see anything wrong here. You upgraded on a route that required 3 e500s so that was what you were charged. I'd imagine you also had an opportunity to sit in Y but made the choice to upgrade. Unless a GA specifically said you'd only be charged one e500, it seems reasonable that you would be charged for e500s on both of your legs (since you didn't get those upgrades within your upgrade window).

I'd imagine you don't have any misgivings about receiving the extra RDMs and EQMs from flying MCI-DEN-ORD rather than MCI-ORD - it's all the give and take of the flying business, particularly in the winter.