Thank you for reaching out to us.
Based on your description, it sounds as though you have chronic staining that does not make you niddah. Though we usually recommend abstaining from relations for about a day from non-niddah staining, this is a precaution against a flow beginning during relations and not a strict halachic requirement. When a woman has chronic staining, we usually recommend that she time relations for when she thinks, based on experience, that she is least likely to stain. So your conduct to date sounds as though it has been permissible.
Still, we agree that this is not a desirable situation. The first course of action is to see your physician about possible causes of staining and to explore other pill possibilities, or other contraceptive methods, that may have a lower incidence of staining.
Please write back with any further questions.