Travel Sites Won’t Tell You:

1. "Don’t assume our prices are the lowest."

Online travel agencies like Expedia, Orbitz and Travelocity profess to help consumers find the best deals, but some experts warn they sometimes fall short. For starters, some carriers don’t participate. And even the cheapest airfare on a third-party website may not beat one offered on an airline’s site. 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."

2. "We’ll snag you a great view—of the parking lot."

Your chances of ending up in a less desirable room increase when you book through a third-party site, says Bjorn Hanson, dean of New York University’s Tisch Center for Hospitality, Tourism, and Sports Management. That includes rooms near the loading dock, the service elevator or a renovation zone, he says. Online agencies counter that their contracts stipulate all customers be treated equally.

3. "Freebies are for our preferred customers."

Many hotel extras, like Wi-Fi and bottled water, may not be included with rooms booked through outside sites. Some hotels also withhold loyalty points, says Tim Winship, publisher of loyalty-program advice site FrequentFlier.com. Sites have responded by offering their own loyalty programs. Expedia’s Hotels.com offers a free night’s stay at over 85,000 hotels for customers who reserve 10 nights. And some work directly with hotels to provide perks.

4. "We’re making the big bucks—at your expense."

Airlines pay fees of $12 to $20 per ticket to so-called global distribution system companies for seats sold through travel sites. But they don’t pay out of their own coffers; the fees are passed on to consumers in higher ticket prices. With hotel stays, the added expense to consumers comes in the form of inconvenient billing: In many cases, a credit or debit card is charged upon booking, tying up the traveler’s credit line.

5. "Our fees are a drain on local tax coffers."

When consumers make a hotel reservation using an online agency, local governments get less tax income than when consumers book directly with a hotel. As a result, cities and counties in 25 states have filed lawsuits alleging that the agencies violate hotel-occupancy tax rules and demanding that the taxes governments receive be based on the amount the consumer pays—not just the amount that the hotel receives from the third-party sites. So far, the sites have prevailed in most rulings.

6. "Advertised prices may have no bearing in reality."

Orbitz, Travelocity and Trip-Advisor have each been fined by the Department of Transportation since July for advertising airfare lower than the actual prices. The companies say they are now compliant with regulations.

Bill Mosley, a spokesman for the DOT, says the agency has been rolling out new rules since last year requiring that ads reflect the full cost, including taxes and fees. Another new requirement: Baggage fees must appear prominently on the site.

7. "Our prices might all be the same."

Shopping around for the best price might not be worth the time or effort—at least according to several class-action lawsuits filed since August. They allege that several booking sites—including Expedia and its subsidiary Hotels.com, as well as Travelocity, Priceline and Orbitz—have been in cahoots with large hotel chains, such as Hilton Worldwide, Marriott International and InterContinental Hotels Group, to charge the same rates. The sites and hotels have either declined to comment on the litigation or say they will contest the allegations. Hilton didn’t return calls for comment.

8. "A price-match guarantee isn’t the same as a money-back guarantee."

To allay fears of buyer’s remorse, some sites offer price matching. But getting the sites to honor their guarantees may not be so simple.

Hotels.com, for instance, claims that customers who find a lower rate elsewhere for the same stay can get a refund for that price difference. But in February, Kaylen Silverberg filed a class-action lawsuit against the site in Dallas County Court, stating that he booked a room for two nights in Rancho Palos Verdes, Calif., for $355 per night and then found two lower prices—one for $223 and the other for $213 a night. When he asked Hotels.com for the refund, it gave him only $71 a night (instead of $142).

Hotels.com parent Expedia says corporate policy prohibits discussing litigation.

9. "Not all surprises are good surprises."

Some online travel agencies, including Priceline and Hotwire, offer another booking option where they hide the name of the hotel and its exact location until after a reservation is made. While consumers can save up to 60% with such offers, they typically aren’t refundable.

Before bidding, but after they know the sparse information about the hotel, consumers should check hotel sites in the same area to see if the price on the third-party site is more affordable, experts say.

10. "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.

Hotels have more control over their inventory, so consumers who book directly are at less risk of losing money if they need to cancel, says Scott Berman, principal and U.S. industry leader for hospitality and leisure at PricewaterhouseCoopers.