It could be that when the killer ripped the eye from Niles' socket, they ended up accidentally taking the eyepatch along as well. In the heat of the moment, they brought the eye along with them and presumably had the eyepatch tucked away when they went to dispose of the eye along with the pitchfork. It's at that time they could've forgotten the eyepatch had been taken in the first place.

Though, that still brings us back to the question as to why they would toss the eye away at the well.

[ ... Unless it's because of something really fucked up ... ]