I recently ran into a similar situation. Expedia gave us a roundtrip itinerary from Houston to Rome with UA and AC segments for a good price. I could not price the itinerary the same way on either the United or Air Canada websites (which priced almost double), but Expedia gave it and ticketed it just fine. We saved quite a bit of money doing it this way, and I still got all the PQDs (ticket was 016 and first segments were AC). It was for premium economy so don't know if that has anything to do with it.