Included in the cost of birth control is required annual exams and pap smears (bi-annually now, I believe) to get your prescription. I hope women deployed overseas have adequate access to doctors and their prescriptions, because I could see that being a large part of it if not.

Also, the efficacy of 96% or 98% is not that impressive when you're talking about large scales over long time periods, since efficacy is measured by the number of unexpected pregnancies per 100 couples per year. CDC estimates that 6-12 pregnancies would result each year for every 100 sexually-active women on birth control. But, since you mention user error, let's assume the perfect-use 98%, which means on a ship of 1000 people would result in approximately 10 unexpected pregnancies each year if we assumed everyone was sexually active and there were half women. Two methods of birth control (such as both genders taking injections mentioned in star trek) would virtually eliminate these unexpected pregnancies, as it does now for people that combine multiple methods of birth control (such as condoms and the pill).

That's not to mention the side effects, which are significant enough for some women to prevent them from being able to take hormonal birth control.