It's never been fully explained what exactly the story is with Stewie Griffin.
Officially, he's supposed to be a baby and yet he sounds like Rex Harrison. Brian can understand him fully, whereas Lois and Peter still effectively see him as a baby. So, yeah, him having a sexual preference for men and women is... weird? Who knows. It's a weird show and it's something that's never been fully explained in a reasonable way to anyone, ever.
Anyway, the reason for all this comes from a recent interview with Family Guy producer Rich Appel on TVLine, where it was revealed that an upcoming episode will dive into Stewie Griffin's sexual identity. "It’s just a two-character episode with Stewie in his therapist’s office for the first time,” Appel explained. "It’s a wonderful episode, and Seth’s performance is spectacular. They delve into all sorts of things you would think would come up in a therapy session with a boy like Stewie. When Stewie’s with his therapist, they pretty immediately address questions of sexuality. The episode covers that, and then goes to deeper issues for Stewie."
That therapist, by the way, will be played by none other than Ian McKellen of, well, Ian McKellen fame. Stewie Griffin's sexuality has something that's been nodded to and winked at for years, but half the fun of it is the fact that nobody's really sure what the story is with it - so you have to question why they're even speaking out about in the first place.
The episode will air in the US next month from March 11th.