We are sorry to hear of your miscarriage.
It is important to note that Seasonique is often associated with more staining than more conventional, monthly-cycle contraceptives. However, any pill can be associated with irregular staining at the beginning of use, so it is probably premature to switch. You should raise your concerns with your physician. (You may find it useful to use our free app, which was designed to facilitate communication with physicians on these issues.)
Most important right now is to know that a hefsek taharah need not be completely clear and not all staining disrupts the clean days. Please bring any questionable bedikah cloths or stains for halachic evaluation. You can also review the laws of stains, as by reading our site's articles "Stains" and "Toilet Paper". Then please get back to us with any follow up questions.