I like Hipmunk's interface better than Kayak's, but Kayak seems to have better data: there are sometimes good fares that appear in Kayak but not Hipmunk, while I haven't found the reverse to be true yet.
We get our data from mostly the same sources, so this should almost never happen. (There are also lots of times we have better rates than Kayak, e.g. on Amtrak and Airbnb, which they don't have.) Next time you see this, could you email contact@hipmunk.com?
Thanks. I didn't know about Hipmunk. I have been using mostly Kayak and, more recently, Google.