Welcome to healthcare magic;
If you had unprotected sex during periods then there are very rare chances of conception.Secondly you have already done pregnancy
test twice and if it is negative definitely she is not pregnant.There many other causes for delayed menses besides pregnancy such as hormonal
etc.Don't worry,complete course of meprate
she will get her periods 2-3 days after stopping the medicine.
I hope this answer is helpful to you.