Depends on what kind of birth control she's on. There is a very small chance of getting pregnant on the pill. Its not uncommon to miss periods or skip days, I just went through the same thing except I missed mine completely which is extremely rare for me. If she's concerned she should take a pregnancy test just to confirm. She can also look up online the kind of b/c she's on and it will tell her on there if her b/c can cause birth defects or not, if she were pregnant. That's what I did.
There is VERY little evidence that the hormones in the birth control pill will cause birth defects. The birth defect hype came from the drugs that were given to women who were ALREADY pregnant, to stop miscarriages. Don't stop taking the pill until a pregnancy is confirmed. It will not damage the zygote.
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