I Believe a issue exists for multi-sector itineraries, for cities with multiple daily frequencies. (at least, I think my issue sounds somewhat related to the OP's)

We recently bought a ticket SIN-TPE, cash J, SIN-HKG on day 1, HKG for two days of business and then TPE on day 3. I believe the underlying ticket was SIN-TPE with a "stopover" in HKG, and the website showed it as "flex" which I think was either J or C. As everyone knows, there are many flights HKG-TPE. But when my my colleague was selecting my Taipei flight, the choice given to her were the first 4 or so early morning flights. Nothing midday, afternoon or evening was displaying; yet that's the schedule I wanted, and obviously CX still has many flights after the morning. I thought that was odd considering we were on a flex ticket and assumed it was some tech bug. Sure enough, upon calling CX every flight in the pm was available for my booking class, just the website couldn't process it for some reason. So it required a phone call to get me on an afternoon flight.