You can have side effects all cycle long (or longer) from the clomid. I remember thinking the same thing you did. Yes, it could DEFINTELY be from the clomid. I had cramps for 40 days straight (even into the next cycle when I didn't take it) from the stuff! Plus the occassional headache. It also made me VERY emotional.
I did five cycles on the stuff so if you have ANY other questions do not hesitate to ask!!