I think people might be confusing the term "humanoid" with "bipedal".
Hork-Bajir are bipeds, which means they have 2 arms, 2 legs, 1 head, 2 eyes, etc. Well, not necessarily all of those, but the 2 arms and 2 legs bit, at least. But being bipedal in itself doesn't make one humanoid.
And really, when you look at just the basic bone structure, there are a lot of similarities between many animals. Disreguaring things with exoskeletons, and snakes and stuff like that, of course. But if you take a look at bone charts, you'll notice that both humans and, say, dogs, have a spine. They both have clavicals. They both have tribia bones, and femurs. They both have hip bones, they both have scapulas. They both have rib cages. They might be slightly different in length and width, but they're still identifiable enough to have the same names.
So, the fact that a Hork-Bajir shares that? Probably just because it's a successful way for nature (or in this case the Arn) to make bodies.