Is there some way I can contact you directly the next time I find an example of this? I'm happy to send you all the diagnostic data your heart desires.
I suspect in some cases it may be due to timeouts or row count limits. I tend to do very broad searches, and then narrow the results with filters. This works great in Matrix, but with Orbitz (which uses the same data source), I tend to hit invisible limits where I can see that some of the rows have just been cut off from the results. (E.g. I can book flights A or B for leg 1, and flights C or D for leg 2, but for the combination I can only book (A,C), (A,D), and (B,C). The B-D trip is in Matrix results but not Orbitz, and this kind of truncation only happens when I have lots of results.
I don't know for sure that Hipmunk follows the same pattern, because I haven't used it in quite some time, but I'm happy to send bug reports IF AND ONLY IF I can have confidence that a real human is reading them.