Unfortunately, it is common to experience irregular staining on the minipill. Some women are able to minimize the staining by taking the pill at the exact same time each day. Other women will still experience staining even if they are careful with the timing of the pill.
It is important to realize that not all brown staining will invalidate the clean days. You should bring any questionable stains to a halachic authority for evaluation. If the stains are problematic and frequently causing difficulty completing the clean days, we recommend speaking to your doctor about an alternative form of birth control. Available options include an IUD, a diaphragm with spermicide, or even combined hormonal birth control. The minipill is generally recommended over combined birth control pills for breastfeeding women. However, if spotting is problematic, combined pills are safe to use and shouldn't significantly affect your milk supply – especially if your supply is well established and your baby is receiving solid foods as well. Any dip in your milk supply can be compensated for by increasing both the frequency and length of feedings.
Please feel free to get back to us with any further questions.
B'hatzlacha!