So anytime I use a basic minecraft command to teleport, or use another mod - like nucelus, command to teleport, I end up with the waystones saying this:

It can be fixed if I put down another waystone and then delete it, which is fine cuz I'm an admin, but is going to pose a problem to users because they have to craft the waystones. Any way that you can look into it and find out why this happens?

The rewrite for Minecraft 1.14 should hopefully fix this issue, but due to the large amount of changes it unfortunately won't be backported to 1.12.

This is not happening to me. Are you using Sponge?