Probably relates to
MC-50129, but I think it might be a different issue.
When I was making a model for the ender pearl and eye, the transparent outer part of the model made the inner parts of the model invisible.
Again, this probably relates to
MC-50129 but I'm not entirely sure.
EDIT - Similar things to
MC-50129 happen in the achievement menu, as the inside of the ender eye renders outside the outer cube.