I have had this happen when I have requested upgrades on some, but not all, legs of a trip.

I once checked in for a "Not Requested" segment of a multi-leg itinerary and was given an F BP. Figured I had been op-upped, but found to my surprise the next day that stickers had been deducted. (The problem was not incorrect data entry up front, because I know aa.com showed the correct legs as "Requested" and "Not Requested.") I considered demanding the stickers back, but decided not to because of the hassle factor and because I had accepted and used the upgrade without asking for clarification.

The same thing happened again a few months later on another multi-segment trip. That time I knew to ask whether the upgrade was complimentary or not and was told no, so I passed it up.

So IME, there seems to be some kind of glitch that occasionally causes the system to "see" a request on non-requested segments, if there is a request elsewhere on the itinerary.