It's pretty common to see this kind of ticket setup with OTAs. You will notice that OTAs often offer combinations of flights from different carriers that you never see on the carrier's own website. This is usually because they are able to price a return trip on separate tickets whereas carrier websites will typically only show itineraries that can be issued entirely on their own ticket stock. These itineraries are not any less "legit", except when you encounter an ignorant agent who doesn't know what to do with them. But they can be cheaper, because you can have a fare component that is only valid on the OAL's own ticket stock, but also only valid as a return trip and allows combination with any alliance partner (or even non-alliance partners) for the return portion, who may have a similar sale fare that has to be issued on their own ticket stock.

As noted by canadiancow, AC is still obliged by its own policies to rebook you to your final destination in this case. Did you pay out of pocket for your new ticket to HKG? Did they cancel your outbound segments after your missed the SFO-HKG flight?