Yes! A few weeks ago, I was looking to get a ticket from NYC to SGN and back, and it was a huge headache. On aa.com at times, I literally could not find an economy fare that would price successfully; any flight combination would just give an error.
I tried many, many times, and sometimes nothing would work, but sometimes I could get a less-than-ideal itinerary to finally go through. Finally I settled for JFK-NRT/HND-SGN with the second leg a JL flight number. The return was all AA numbers (SGN-NRT-ORD-EWR).
So my only advice is keep trying, settle, or likely both.