So, first, a penis in a vagina unprotected without a condom is risking pregnancy. Even if there is no ejaculation as the penis emits small amounts of sperm which is enough. However, you DID use a condom (good job), so would not be concerned about pregnancy. Condoms can fail and that is why you read that pregnancy can happen when using condoms but that is usually really noticeable. Condoms split wide open when they do break. So, I would guess she is just late which happens from time to time to all women. It can happen due to stress, changes in routine, illness, weight gain or loss, etc. good luck (ps: she can always take a home test just to be make sure, but expect it to be negative).