The eyes seem normal to me. In any case squids belong to the exclusive club of animals that can have different types of eyes (different size or shape) at the same time.
From the article: The protein encoded by TDO helps to add pigment to the animal’s eyes and chromatophores
Yeah it really looks like the eye pigments are not the same.
They aren't, and the article notes as much.
They removed the dots in the eyes as well.
So it’s blind? Reminds me of the Invisible Man plot hole where the guy gets turned invisible and thus his retinas also become transparent and therefore he shouldn’t be able to see anything.
Not necessarily. The animals in the photo aren't the same animals. This is the normal aspect of a squid larvae.