Thank you for your query at DoctorSpring.com.
Firstly, you are not considered late until you finish ALL of the pills ( including the placebo ones ).
It would be clearer to me if you mention the EXACT date of her last menstrual period, and the general cycle length.
As she is still on the placebo pills, she is not late going by the pattern of birth control pills.
When you are on BC, you do not ovulate ( mostly speaking ).
Birth control is 99 % effective as a contraceptive, and it acts as a contraceptive, by interfering with ovulation. The fact that it is 99 % effective, and not 100 % , means that SOMETIMES, albeit rarely, ovulation CAN occur while on BC.
Some antibiotics do interfere with the pills, reducing their efficacy -a specific name would help me guide you better, which particular antibiotic was prescribed, however it was for only 3 days, and as long as she took the pills sincerely for the whole pack, on the whole, she stays protected.
Ejaculation inside the vagina a day or two before the expected period has LESS chances of pregnancy, chances are maximum mid cycle, when ovulation occurs, if at all it does, while on BC.
Stress CAN cause delayed periods - as can anxiety, hectic travelling, change of climate or altitude, thyroid disorders, polycystic ovaries etc, and once in a while a delayed period might be just that - a delayed period, without any other implications, as long as it is a one off event, not a pattern. I would not worry right now.
Going by what you have described, she is diligent with taking BC, and chances of pregnancy ( honest opinion ) in my view are quite low.
You should repeat a pregnancy test ( you know that the one you took was too early , and hence irrelevant ), and that should be done once she finishes with her placebo pills, starts her new pack for a couple of days, and still fails to have a period.
I hope this answer helped you. All the best. I would be happy to address any follow up questions.
Yes, protected sex is best for both of you, BC notwithstanding.