Can oral birth control pills permanently affect a womans fertility after stopping it? my wife still hasn't had a normal period months after stopping.

No, not at all: The oral contraceptive pills will not change your fertility as this is an old myth from the days when the higher dose pills were used extensively. Patients who had irregular anovulatory menstrual flows were often placed on the pill to "regulate" their cycles as young women. Then when it was stopped to get pregnant,, their periods went back to their previous irregularity and the pill was "blamed".