The systems need to be changed to instead of just check for fares, check to see if there is any availability for those fares. Kayak goes out and checks the fares for certain dates and returns what the airlines tell it (or have told it, they may not even be checking real time).

Though when an airline cuts off a low fare, that's also why for a few more hours you may still be able to score it at a Kayak, Orbitz, etc.

When you go to book it, they now say I need four seats and the airline comes back saying sorry, we don't have four at $1000 each, but do have four at $1500 each. You want them?

Also if you are booking multiple tickets, remember that most engines will price them all the same. So if you need four tickets and the airline has only three fares at $1,000 and then they go up to $1,500, you will be quoted $1,500 for four fares, not three at the lower price and one at the higher price. If booking multiple tickets, price them individually in addition to as a group, sometimes you can get one or two at the lower price.

As they say in their terms

You agree that KAYAK is in no way responsible for the accuracy, timeliness or completeness of information it may obtain from these Other Guys

Which is sometimes one of the hassles of using a third party site, you can sometimes get great rates until you actually try to book them and then those rates are no where to be found.

Kayak is by far one of the better places in that aspect, there are some engines that are just silly about it, you can never book the rate they come back with.