I've entered to the end in my pre-1.9 world, (a world downloaded from my Realm Trial), respawned the Ender Dragon, killed it, and gone through the end gateway. So far this was normal, except when I've tried to go back. When I've thrown the ender pearl to get back, I got back... to the far islands again (I mean, it just reloaded the place where I already am). Testing in creative mode, it teleported me inside a bedrock block (the one on top of the gateway)
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@unknown,
He didn't teleport inside the blocks while in survival. The issue is that he wasn't teleported or he was teleported to the same place he was before.
Teleporting inside blocks isn't WAI, it's MC-2164
@unknown, do you still (1.10.2/16w36a or later) have the issue?
Oh, sorry, yes i see that, One in survival, other in creative...
Can he try throwing the ender pearl sideways into the portal?
Ill get back to this when i test this bug a bit.

Forward-resolved in favor of better explanation in MC-114566
You threw your ender pearl up, it landed in the block above the other portal.