Yeah, at that age you can't absolutely tell a little trans boy from a budding lesbian from a straight tomboy. I don't think anyone can, even the kid, until puberty starts to hit (even then it's not absolutely cut-and-dried for all of us). The girls seem to be somewhat clearer about it, possibly because gender role restrictions on male-bodied people are enforced so much more strictly. But I know more than a couple lesbians whose baby pics look just like Shiloh's. If you're not a celebrity kid, nobody cares.
But there's a chance s/he might be trans, which is also fine. I wouldn't wish transness on anyone, but if anyone has the resources and support and love to handle it, it's the adorable little child of Brad Pitt and Angelina Jolie.
