While testing the fix of MC-3, I found this bug. I then tested it back in 1.8 and it was still there, so I don't know how long it's been around or even if there is a ticket for it already (I tried to look it up but couldn't come up with anything).

Anyways, when you travel to the Nether, generating a new portal, and build a new portal, even just a couple blocks away, and destroy the old one, the overworld portal doesn't adjust your destination coords in the Nether, placing you where the old one was.

To reproduce, build a new Portal in the overworld and travel through, generating a new portal in the Nether. Now build a second portal in the Nether a few blocks away and destroy the first. Now if you travel through the new portal to the overworld and then back again, it will place you where the old portal was, even if it was destroyed. The game also neglects to generate a new portal in that location, so you just spawn in with no portal blocks touching you.