As you already know some amount of pain in lower abdomen is normal in pregnancy because of stretching of the ligaments and muscles of uterus.
With your case I suspect this pain more than normal one .Such symptoms are manifested in ectopic,pelvic inflammatory disease and if there are any cysts or adhesions in the uterus.
You need to consult your gynaecologist for further tests as the pregnancy tests show a negative result now.
In case, the pain increases or there is any discharge of blood you need to shift to ER as soon as possible.