It's very common for birth control pills to change not only the timing of a period, but also the consistency of the blood. It's no longer an actual period--instead, it's a "pill" period, which means that since there is very little uterine lining to shed, the blood is mostly withdrawal bleeding from going off the active pills and starting the placebos. It's also common to have breakthrough bleeding between periods, especially in the first few months of taking the pill. Chances are everything is fine, and her periods may become regular as she gets adjusted to the pill. If you're really worried, she can take a home pregnancy test, but if you were using condoms and she's on the pill, she's most likely not pregnant.