It seems I've had the most changes in fare price or availability when identifying flights on United specifically, more so than any other airline, in my experience. That being said, it's still pretty infrequent given the volume of airfare we've booked through it for our people over the last 2 years or so.
Another thing I would add is that in connecting flight situations, it will occasionally present an itinerary that's technically possible to make, but not always entirely practical or ideal. (e.g. the window between flights is really narrow, not leaving much margin of error for flight delays, getting to another gate/terminal, etc., if not near the one you arrive at.)
All that being said, it really does work pretty great and we prefer using it to any of the other travel sites.
I would love to know why there are occasional fare discrepancies though... as far as I know google treats the click-through to the carriers' sites like an ad click, so I don't think Google is "marking it up," rather, the carriers are in some cases pricing based on the referer link or something. It can also be a demand pricing issue too, as the flight fills up, I suppose. My understanding is that Google is basically just the informational conduit between the user and the airline so it's weird that there are occasional price discrepancies.