If they are unintentional transparencies then just open the skin in paint (Paint doesn't support transparency) and save it, if you have transparent bits on the hat layer that you want just remove the colour in a different program.
You could have accidentally lessened the opacity of certain pixels when shading/changing a shade of colour. :P (Sorry if this doesn't help and I'm just talking nonesence I don't know much about computers and I'm only 13).

they meanies

I doesn't upload skins made from scratch how could they!