Many transactions are processed offline. It's impossible for banks to prevent cards going at least slightly over limit in those cases.
Quite a number of organisations (eg. rental cars and hotel rooms) put a pseudo-transaction in for an inflated amount of money when you present your card to them but only charge the real total to your card when you finish using their service. It would cause enormous inconvenience to users if banks didn't allow users to apparently go overlimit in those cases, since the amount to appear on the statement may in fact not be enough to go over the limit.
In the end, it's up to you to know when you're getting close to it. That said, the banks simply stand to get more money from you if you do exceed the limit, so the fees they put on this are purely a rip-off, just like cash advance fees.