Originally Posted by
NYC Flyer
Agreed. There is nothing particularly unique or uncommon for there to be a fare break at a connecting city. If the itinerary is less expensive this way, the GDS/CRS will price it as such. It's still a valid O&D ticket (assuming one does not intentionally purchase separate tickets), and there should be no with issue checking bags/IRROPS, etc.
The issue was the fare break was at a different city than OP expected. Yes, there are frequent situations where you can end up with a broken fares for an A-B-C routing and not realize it (and assume you are getting an A-C fare). As long as connection is less than 6 hours, you can either check through from A-C (which is what will typically happen without input) or short check at B. But OP's situation is different as the A-B-C-A routing had a fare break at C, with no break at B (which OP had been expecting since B was chosen as the "destination" in the roundtrip search). Having the break at C instead of B was possible because of the less than 6 hour layover at B and is what is created issues with the short check.