From experience, I'd guess the most common problems are lack of consistency, hiding of the system state and failure to design for error. Being intuitive, however, is a two-edged sword. The good news is that users learn the interface quickly and make fewer errors. In addition, an intuitive interface is more likely to be properly operated when the user is under stress, the time when people unconsciously fall back their innate and highly learned behavior. In safety critical situations, this is not always desirable.
People have a tendency to minimize their workload by using more and more general cues.
For example, instead of reading a red warning label, they may learn to simply respond when they see the red text - it is much easier and faster to recognize color than to read text. If there is an unusual or unexpected message in red, the user will not notice the change because the cue is color, not the actual text. Several patients being treated with the machine accidentally received fatal doses of radiation. In the original version of the machine, the operator had to enter control parameters twice. Second, the user entered the values into a control panel.