I learned several years ago not to use any of the travel sites for this very reason. When something goes wrong, neither party wants to help you, even when it's something that should be far easier to resolve than what the OP dealt with. All you get is finger pointing back and forth.

Expedia's customer service is horrible.

Expedia and similar sites have good prices, but I've found that I get similar prices booking directly with the airlines. Most importantly, I don't have to deal with the nonsense that occurs when something goes wrong.