When creating a Nether portal in the overworld, going through it, then going back through generates a new overworld portal instead of coming out of the portal you just went through. Portals will not link correctly. Reproducible 100% of the time. I attached a video of what happens. I have also attached a download link to a copy of the world file.

Video: https://youtu.be/XYOnAfBg_10

World File: https://www.dropbox.com/s/zdgzsbd3jbc48ww/Enderman%20Nation21.mcworld?dl=0