Who do you think owns the red eyes? Could it be Discord, or one of Luna's batponies? Luna "oversees dreams", and Twilight has told Flash that. Will Flash suspect Luna knows his love for the Princess of Friendship? Twilight also told Flash the red eyes could have been one of the batponies. Was Luna sending one of them up there to keep an eye on them? It was cheeky to watch them on the night of the aurora. Luna may be more sympathetic to their friendship and love than Celestia, since Luna fell for Discord a little over a thousand years ago.

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Batman.

I am sure Batman does not have red eyes, Apache. Didn't your name use to be Apache?

There is widespread agreement that it was Discord. Although Erico and Broman appear to agree it was Luna's red-eyed Thestrals.