I don't have personal experience with your exact scenario but I have paid for F&B at hotels when on a points stay and received the expected Bonvoy points on my account for this expenditure when the stay posted including the elite bonus. I would have expected that the upgrade fee you paid would be treated by the hotel similarly and therefore attract Bonvoy points when the stay posts however the fact that it didn't maybe indicates the hotel treated this transaction as something else that isn't tagged as eligible for Bonvoy points. This doesn't make sense or seem fair but it could be what happened. If you have the folio and it includes the additional upgrade fee then you can try submitting to Marriott customer service using the missing stay form to see if they grant you the points.

I've never booked a (points + cash) rate through Marriott but they exist and are generally considered ineligible nights during bonus season but maybe someone who regularly books (points + cash) rates could comment how many Bonvoy points they ultimately get from such bookings - does the cash element attract points or not when the stay posts? At first glance, this would be a similar scenario to yours but the way Marriott's reservation system and the hotel deals with the cash upgrade (and hence the cash portion of your reservation) is quite different so I still think it's worth submitting the missing stay form if your folio reflects the additional expenditure. You won't lose anything anyway.