First of all, it is important to realize that not all stains will render a woman niddah. Stains found on colored underwear and on disposable pantyliners may be disregarded. Stains found on toilet paper may be disregarded as long as at least a few seconds elapsed after urinating before wiping. See our article on Stains for more detalis.
If it is difficult to manage with the staining despite the leniencies of ketamim, we advise consulting again with your doctor. While it is not uncommon to experience irregular staining from hormonal birth control, your doctor can check if there is any other cause for the staining (such as a polyp or cyst, irritated cervix,etc.). Additionally, you can speak to your doctor about trying a different method of birth control. One possibility is the combined pill with a higher dose of estrogen, which often reduces irregular staining. Another option is to use a diaphragm with spermicide. See our article on Choosing a Contraceptive Method for more details about these and other methods, and get back to us or your doctor with any further questions.
B’Hatzlacha!
This response has been updated to reflect the rulings of our current Rabbinic Supervisor, Rav Kenneth Auman, regarding waiting before wiping.