Not sure if this is the case here (as its likely a question of codeshare rules) but D582 posted an excellent explanation a few years back on how airlines use more complex and dynamic pricing model that consider individual flights and connecting inventory differently.

Theoretical example: A YVR-YYZ-DXB flight. Both the YVR-YYZ and the YYZ-DXB segments may show availability in M, but the full ticket YVR-YYZ-DXB will offer M space on the same flights for the whole itinerary. I've mostly noticed it for connecting overseas flights through hubs. Theoretical example again: YUL-YYZ-BCN. AC will sell you cheaper fare if you fly YUL-YYZ before the late-afternoon peak business travel times, even if that fare class is available on the single segment. They know that they can sell the 5:00pm YUL-YYZ seat for a lot more than the value of the segment as part of the YUL-YYZ-BCE flight so if you want the connecting during busier times, you will beed to pay more to get it.