Nether portal will randomly be unlit. This cause portals to teleport you to the wrong portal. When entering the nether portals with randomly become unlit.

When entering nether portal to go to the nether it will sometimes unlite and you will be enter through a different nether portal.

 

[Update] I'm pretty sure this is an issue with loading a 300+ MB world. We were able to reduce the size of the world and we haven't had  the same issue since.