Normally, entering an End portal creates an obsidian platform at y=48 and teleports the player to y=49. But if you create an End portal in the Nether (e.g. using creative mode), it instead creates it at y=49 and teleports the player to y=50.

An example of why this is a problem is that it leads to builds around the platform appearing to be offset depending on which dimension you enter from (which is irritating for me as a mapmaker trying to use all three dimensions–I have to use commands to fix this in my map).