Based on the data points on this thread, I think the issue might be the mismatch between QR and AA units for baggage allowance. For flights to/from the US and/or Africa, both airlines allot baggage by piece. For flights to all other locations, Qatar uses a max weight allowance (any number of bags as long as it's within a total weight limit), while AA still allots by pieces. If this assumption is correct, segments to/from the US or Africa should have proper baggage endorsements while other tickets can expect the problems.

As an aside, after I got my baggage endorsements issued properly, my flight was re-ticketed due to a schedule change and the correct baggage endorsement is still reflected in the newly ticketed itinerary, on the QR app and the website. So at least it sticks once it's fixed...