Are you finding the same specific flights have different prices on the two services, or are you finding that Hipmunk is able to find flights that Google doesn't?
(Disclaimer: I work for Google, on an unrelated project.)
(Disclaimer: I work for Google, on an unrelated project.)
In general, I based my original comment on what Google Flights show as the "Best Price" vs what Hipmunk is showing as "Best Price." And there isn't any filters on either platform that would be quick to explain why the huge price difference.