Teenagers can be sneaky.
Probably he did what I did when I was young and went in through the window if the girl was on the first floor. Then ninja sex.
Of course at that age, we didn’t have actual sex, just about everything shy of that. That happened AFTER she moved out in her own place.
Unfortunately, a similar thing happened to me when my daughter was in her teens. I was a single parent, and the BF would wait in his car down the street until he saw my car leave, then would come by. I figured it out by putting a keylogger on my daughters computer and reading what she wrote on chat with her friends. Whereas I never “caught” the boy, I did attempt to file charges (since she invited him in, even though a minor, I could not), so I got a restraining order against him. This caused a huge amount of discord between my daughter and I that resulted in her running away to her mothers house for 3 weeks, missing school, and subsequently screwing up her HS GPA because she fell so far behind. She is an adult now and we have a fantastic relationship, and really regrets this series of incidents, because she can see now that the boy was raping her even though it was “consensual”.