“Don’t assume our prices are the lowest.”

Online travel agencies like Expedia, EXPE -1.57% Orbitz and Travelocity profess to help consumers find the best deals, but some experts warn they sometimes fall short.

Travel sites say they offer exclusive deals. But Joe Megibow, a vice president at Expedia, says, “I can’t say 100% of people 100% of the time will always find the cheapest rate.”

“Adding complication to cancellations is our specialty.”

When customers use travel sites to book rooms, the amount of time they have to cancel the reservation and get a full refund can be more limited than if they reserve directly with the hotel, and in some cases there is no option for a refund at all, says Mr. Hanson, of New York University.