Welcome to HCM.
Chance of pregnancy
is there,if intercourse is done around ovulation time in regular cycle.
Pain and cramp during urinating may be associated with some sort of infection. Do a Urine test if persist for 2-3 days or more. Drink plenty of water and maintain personal hygiene.
Spotting or slight bleeding may be due to hormonal
imbalance or early implantation
Do a urine test for hcg after 1 wk of missed period or a USG lower abdomen to rule out something.
See result and consult with doctor. Avoid stress
and practice safe sex in future.