Your intermenstrual spotting and sometimes clots seems to be due to hormonal
disturbance. Since you have stopped using (contraceptive
) pills for about 3 years, this cannot be related to the pills.
If the eggs are not being released it may lead to the excessive thickening of the lining of the uterus
(Endometrium) which can break in between causing some spotting to bleeding.
The other causes could be some small growth inside the uterine cavity
. But usually such growth cause excessive bleeding rather than spotting.
Please get your thorough work up done along with ultrasonographic study an endometrial study. It is likely, you will require some cyclical hormonal treatment for few months.