Touch up fail?

Seams should have had latex caulking, nail holes could have been filled with Fast and Final so there was no flashing.
That whole thing needed two coats of paint anyway for the paint to hold up.

Well, we pros debate this regularly and the consensus is: There's no such thing as a touch-up, well, at least a seamless touch-up. Even if you use the exact same paint from the exact same can, it's still going to stick out like a sore thumb. You are adding another layer which creates an ever so slight ridge that is not noticeable from a distance, but, up close can be very noticeable.

You approached it the right way.......primer, then paint, but, it's just one of those things that's next to impossible to accomplish......the seamless touch-up. Another full coat is the way to go. It won't take you long.