Yup, even when the front page for the hotel (or airline) claims to "always have the lowest rate". Sometimes you can call and negotiate a price match, but it's easier to just book through the online agent. Since online prices are occasionally unavailable, it's most reliable to actually buy online, then negotiate a better price directly, then cancel the online booking, but this is borderline abuse of the online agent and you have to be careful with the cancellation policy.