Sounds like you had some grit on your cloth when you wiped the screen or something sharp struck the screen which scratched it.
There's not much you can do once the scratch has happened. While a fine polish can lessen the scratch on a glossy screen the retina screens aren't glossy, they have a fine matte finish so polishing the screen will create a higher shine bloom were you rub which I think will look worse.
To prevent damage use a proper screen wipe and make sure to keep it clean.
I use two the first is a 3M micro polyester to dust the screen I fold and roll it so I can drag it across the screen with very little pressure to snag the heavy dust and grit and then I use canned air to blow the loose stuff away. Then I use a second eyeglass wipe (smooth polyester cloth) and using a cleaner spray (spraying the cloth, not the screen!) wipe the screen to remove any grease marks.
Make sure your case is clean and closed tightly when you travel so road dust doesn't get inside (the gritty stuff!). I use a stiff artist paint brush to get things loose and use canned air again to blow the stuff out the vents and keyboard keys. Make sure to do this outside. Why make more house work for your self or partner ;-}