Taking birth control pills early during pregnancy doesn't seem to cause birth defects, but if you do conceive while on contraceptive, there can be an increased chance that the pregnancy will be ectopic. As a precaution, if you suspect that you're pregnant, do take a home pregnancy test and if tested positive, stop consuming birth control pills until the pregnancy is confirmed. If you have concerns because you were on a contraceptive before realising that you were pregnant, talk to your gynaecologist to find out more.

Reference: http://www.mayoclinic.org/healthy-lifestyle/pregnancy-week-by-week/expert-answers/birth-control-pills/faq-20058376/