Contraceptive Pills after missing period

Hi, My girlfriend and I had sex on Sep 14, 2018 after she had her periods last week of August. Since then, she did not get any periods until now, i.e, she skipped two months. We did multiple urine and blood HCG tests to ensure she was not pregnant. The HCG level was below 1.2 We had sex again last night but this time we realized at the end of the act that the condom broke, however I had not ejaculated at all. We are scared about whether or not we should pop a contraceptive like iPill right now to be safe? The last time we took iPill, her periods skipped for two months. This was in April 2017. So, considering her PCOD and also the fact that she has skipped last two months, is it advisable to take iPill which slows down the periods even more? Please advise.