[ Causes and Solution ] Stain in Retina Display

Those are keyboard key marks from finger oils transferred to the screen. Something has like eaten away a part of the screen.

Yes, acid on your fingers (and oils) transferred to the keys, then to the display when closed. You may have thought that somehow my retina display got some weird clear-ish stain damage . No, that's stripped AR coating from the screen,  not  ON THE SCREEN. You're thinking it's something there, when its something missing.

Your hand oils and acids have stripped the AR coating off part of the screen. Keep cleaner hands when using your Mac.

Some people have naturally VERY HIGH acidic skin excretions,  you may have this issue.

SOLUTION

There is no that can recoat a glass display while attached to the display assembly.

That coating is applied in a vacuum chamber , you cant "recoat" it, and if you could, which you cant, it would look horrible and not stick.

You can only apply said coating on NEW sterile displays in a vacuum chamber.
You can only see that damage on your display if its in a well lit room / outdoors......., in a dark room I dare say I bet you cant see the 'damage' at all.

So, the best idea is to take precaution before . Again remember Keep cleaner hands when using your Mac.