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.
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maybe has something to do with "cull"?

Yes. Adding cullface did fix the problem. Thanks.