Originally Posted by
PLeblond
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.
O&D availability is likely irrelevant here (based on spot checking). You can always rule out availability issues by unchecking the "Only show flights and prices with available seats" checkbox in matrix.
Codeshares are also irrelevant, as there are filed fares that allow AC and EK flights from YVR to ISB with no codeshares. Example: Nov 20 AC78 EK612 to Nov 28 EK613 AC79.
There's nothing wrong with this, so I'm not certain where the thread premise came from as even AC's site can handle it. Confusion may have come from the service not being daily and/or an unavoidable long connection time on the return leading to AC's site suppressing the one-stop result (but that's >30h anyways so I'm not sure what option OP is referring to.. will need flight numbers to look into it).