PCOS causes not only problems with menstruation but also with ovulation, and anovulation, as it happens. When you're on progesterone therapy, you can get spotting due to hormone level instability. Spotting is a common sign of changes in the female body but usually is physiological. Except in rare cases, spotting during progesterone treatment is not a big deal but you must continue to follow all the prescriptions and keep your psychiatrist informed as well.