Definitely this. I have one lecture where I have students install some packages, just to see how it works, but everything else uses pre-defined Project.toml and Manifest.toml that students then instantiate.
I make sure students are all installing the same version of julia as me, and I did not encounter any issues, even with windows users. At minimum, you should make sure they’re using projects for everything, then usually it’s easy to reset by just deleting the toml files (though in practice, I’ve never had this issue).
I can’t even imagine what they’re doing that could bork their registry, but it should be as easy as removing the .julia directory, then launching Pkg again.