It depends on what you are seeing. Are the spots smoother than the surrounding wall or is there a sheen difference? What is making the spots stand out?
When patching walls and ceilings you need to pay attention to the texture that is present. Even smooth walls have a texture left behind from rolling paint on the surface, roller cover stipple. If this is the case you can take a little drywall mud and mix it in with a little Kilz (acrylic only). This mixture can be rolled over the spots to give them some texture, roller stipple. This is best done with a mini-roller.
If the spots stand out from a sheen difference, shinier, then just give everything time to cure. This effect should diminish after a week or two.