Upgrades at the airport are subject to availability of both seats and catering. At outstations this may be more of a problem than at DOH, so they may have been correct on that.

https://www.qatarairways.com/en/upgrade.html

Nobody will be able to give you a definitive answer to the upgrade in advance question. It's possible the system was looking to upgrade the whole itinerary into First on a fare difference basis but couldn't because there was no F cabin on the US sector (hence not eligible / none available). You usually can not upgrade just one sector unless you receive a targeted offer for that sector from QR, or ask at the airport. Or perhaps they were expecting to swap the aircraft to one without an F cabin so were not offering upgrades at all.

It's disappointing but sometimes a risk of booking members of the same party on different reservations.

For future reference, at airports other than DOH it is usually best to seek out the station manager at check-in for something like this. They are likely to be employed by QR and know all of the policies. Pretty much everyone else you deal with at an outstation will be employed by a third party and potentially not only not be fully aware of QRs policies but possibly also liable to confusing them with those of one of the many other airlines they handle. This is true for most airlines at remote outstations.