Upgrade awards are awards, and subject to the $75 expedite fee (waived for elites). This has been the case for a long time.

http://www.flyertalk.com/forum/ameri...ssing-fee.html

You should not have been placed in F, if you booked Y on a 3-class plane. But mistakes happen, and they usually get corrected before you get to board. If if it really missed, then you should enjoy your F seat and the elusive double upgrade