Can Birth Control Pills Cause Harm To The Foetus?

i have hypothyroidism for the last 2 years.i had eltroxin tablet for 1 year...then i went to different doctor...he asked me to scan my uterus...based on the scan report he said estrogen hormone is less for me...so he asked me not to get pregnent for 6 months...he adviced me to take femilon tablet...but i'm taking femilon for the last one year(till this month) insteed of 6 months...we r planning to get pregnant next month...i stopped having femilon till this month...is there any issue in gettig pregnant next month?is there any side effect or growth problem for my baby bacause of having femilon till this month?please advice me on this...Thanks