I have no idea if this bug is also present in the betas but what I do know is that this is a major issue regarding Nether portal linking in the current version of Minecraft.

In my world, I created a 5x3 (height and width in blocks) Nether portal using lava buckets inside a man made cave and went through to travel around the Nether for a bit. I then went back to my portal to return to the Overworld but was not teleported back to the portal I created in the Overworld. Instead, I was teleported to a taiga over 100 blocks away from my nether portal.

When I returned home, I entered my nether portal for a second time for an experiment. As usual, I went to the same Nether portal that was created when I first entered the Nether but when I entered the portal again, I was teleported to the same portal in the taiga, even after I destroyed it completely in Creative after making a backup copy. The screenshots (taken in creative) will show the portals I am talking about as well as their coordinates when I stand in them after deactivating them. The seed is -1512140161.