Hello Anon703, my name is Noelle. I am 14 years old, I am sorry to hear about this uncomfortable experience. I do think that you should confront her on the matter and share your feelings on the subject. However, if you do talk to her try not to make it sound like you are attacking her- just let her know that you love her and you are concerned about her. Just know that sometimes people make mistakes, relationships can be complicated. Be compassionate and understanding. Good luck.
Depending on your relationship with your sister you could sit down with her and see how she is doing and if anything is going on in her life. Unfortuently, technology has allowed for people who are too young to engage in this behavior. At the same time your sister is young and not yet mature and assuming her boyfriend is around the same age are curious about their sexuality. Also remember you are not the parent and though you love your sister it is a parental obligation to discuss such issues. All in all I would just see if something is up but if your concern won't dissipate telling your parents might need to be done and hopefully they can approach the issue without implicating you or what you saw.