You see those kind of skull abnormalities with deformed babies a lot, if you look up "birth defects". A lot of still born, birth defect riddled babies are born with the splayed, overly large skulls.
I've been to the Mutter Museum in Philadelphia and you can see some interesting birth defects ( preserved in glass jars ) downstairs with the "dead baby display". (
http://www.collphyphil.org/mutter.asp ) I just have a feeling that the majority of alien skeletons people find are merely deformed human children. The skeletons are usually small because, due to their deformity, the children die young or at birth.