My girlfriend has had her period every two weeks ever since she started her periods, that was 3 years ago and she is now 15. But she missed her last period and is now two weeks late, (a month since her last period exactly), she has been having creamy/yellow discharge that smells odd she says, could her hormones be setting her period straight or is she pregnant

She is having sex, I take it?
A woman having sex can always be pregnant, regardless of symptoms.
What have you been using for birth control?
Getting her period every 2 weeks for 3 years puts her in a very unusual category. She might be normalizing, she might be pregnant.
Smelly yellowish discharge might be a yeast infection.
It's time she saw a gynecologist anyway, to be examined for the frequent periods, and the discharge.