Whoever did the repaint might have edited the prop texture & messed up the transparency. There should be no need to repaint common parts. If you can find the original aircraft use the prop texture from that.

Without knowing which particular Bf 109 you have or which sim it's for I can't comment. Some aircraft have transparent prop textures, some don't. It depends on the designer & which design program was used to create it. If it does use a prop texture maybe this wasn't included with the repaint.