My son has had three tiny marks in the corner of his eye since he started on Nutramigen. At first looks like scratch marks, but you get close and realise they aren't scratches. I have never thought of it as being connected to the milk, for some reason, as they don't give him discomfort and they aren't spreading.
Perhaps a trip to the GP, as usual with photos in case they aren't visible when you go, and notes about when you notice them appearing and/or disappearing. Always best to have them checked out!
And, happy that he's eating well for you!