It's the nature of photography compared to the eye, I'm afraid. A photograph will necessarily be of a higher resolution than looking at the model with the eye, so it will pick up things the eye can't see. Do you use a magnifier/magnifying glasses at all? They will help to a degree (mine certainly did), but you're petty much always going to think it looks better just eyeballing it than taking a photo.
It's probably worth pointing out that layering isn't the be all and end all of painting techniques (though you're also probably well aware of that). Certain other techniques will achieve better transitions (glazing, blending, etc.), or will help improve the transitions of your layering. It doesn't matter how much you paint, there's always more to learn and ways to improve. If you feel like you've hit a plateau (we all do at times), try new things, watch youtube videos on special techniques you've not seen before, and so on.
Nice Batman,
btw!