We investigate the difficulties that advanced undergraduate students have in understanding quantum measurements and time development toward the end of a full year upper-level quantum mechanics course. Our analysis is based upon a test administered to 89 students from six Universities and individual interviews with students. We find a number of common difficulties by analyzing the student responses. It is striking that most students shared the same difficulties, despite the variance in their background and the variety of teaching styles and textbooks. Concepts related to stationary states, eigenstates, and time-dependence of operators were found to be particularly difficult. Analysis of test results suggests that the common misconceptions originate from the tendency to over-generalize concepts learned in one context to another inappropriate context.