You didn't mention what brand of paint you're using. Some of the paints on the low end (Cheap $$$) of the scale will be somewhat translucent, especially metallics.
The reason your patch is darker is because the second color coat was sprayed over a darker color than the first coat. If you had used a light gray sealer you probably wouldn't have had this problem.
The best fix I can offer is to let it dry scuff and use a good compatible sealer, as close to the primer color as possible, then recoat.