I think I know why DJ Pon3's eyes were thought to be red. It's the most plausible theory I can come up with, anyway. Vinyl Scratch's eyes were thought to be red because she closely resembles a fairly popular anime character with her blue hair and tendency for a wardrobe that favours white. Tenshi Hinanai (Hinanawi?) shared these chromatic features with DJ Pone, and it is entirely possible that fans of MLP:FiM who also share a liking for Touhou to make this connection. BlackGryph0n's fan-made animation of Vinyl Scratch certainly cemented this fan-canon info within the fandom until it was debunked at the finale of Season 2. This is more than likely just a coincidence, but until I'm proven otherwise this is my best and only explanation.
My second guess is that several ponies' general colour schemes slide 3 units on the colour wheel. For instance Applejack has an orange coat, blonde hair, and green eyes. Apple Bloom has a pale yellow coat, orange/scarlet eyes, and red hair. This logic was probably shifted over to Vinyl Scratch. Her white coat is ignored since white (and black) goes with anything. So cyan/blue hair, purple glasses, and red eyes was a logical transition. Come to think of it that sounds a lot better than my first theory. God dammit, I drew Vinyl Scratch dressed as an anime character for nothing.
Background from: [link]