What Causes Vaginal Spotting After Missing A Period?

my fiance and i believe she is pregnant, her period is 3 weeks late and she has variosu signs of pregnancy. like breast getting larger and harder, she has been getting alot more tired lately and has had a increase in apetite. but we've taken two home pregnancy test and they came back negative. but now she having vaginal bleeding but very little. what the chances she pregnant? please explain more to us as well thank you