What Causes Irregular Periods After Taking Clomid?

Hi, TTC for our 2nd child. I ve done HSG, found out my left fallopian tube is blocked. my doctor said most probaly both were blocked and by the force of the HSG procedure it had the right tube opened. At the blockage or adhesion was beace of my CS birth on my 1st baby last May 2014. I ve done my first round of 50mg clomid (taken day 3,4,5 of my cycle), I m already on my CD31 and ive been taking HPT and its keep saying negative. I m already 3 days late. My menstruation was never irregular till took clomid. Does this mean its just a side effect, or this still could mean im pregnant and just have to wait some more days before checking again through HPT. If it is just a side effect, is there anything i can take to regulate my menstruation cycle again? Thanks.