Can amoxicilin antibiotics have an effect on the menstrual cycle when taken alongside contraceptive pills? (late period but not pregnant)

Possibly: not usual; however any mediciation can alter your cycle-rarely amoxicilliun.

Not the antibiotic: Antibiotics do not affect your period. The amoxicillin did not make your period late. It is not entirely clear whether they affect birth control pill effectiveness, although it is common to recommend using a backup method in that situation. Good wishes.