(I'm glad her period came, but it really did sound like you were worried for nothing.)
Sweetheart, if you are this freaked about fatherhood, use condoms along with the birth-control pills she is taking. It's a good habit to be in anyway, because it reduces the exposure to STDs,
Stress can do it, for one.
I think she is not pregnant.
Only read a pregnancy test within the prescribed time period. Evaporation lines hours later do not count.