As you did sex on 3rd day of cycle, then there is no chance of pregnancy
as it is safe period.
There are other possibilities of irregular spotting like hormonal
imbalance,stress/anxiety, thyroid problem, wt gain/extreme loss, irregular eating habits etc.
Need to investigate properly to rule out underlying pathology by USG lower abdomen,Thyroid profile,LH/FSH etc.So consult with your doctor and take suggestive measures.
To conceive, you have to do unprotected sex around ovulation time which occurs 14 days before due date. You may use ovulation prediction
Avoid stress,take healthy diet with Vit-E & Folic acid
supplements,control body wt & proper sleeping.