Painted sample areas have different sheen than the rest of the wall
Did you just apply primer over the paint sample areas? If so, the primer left the wall in that area with a different surface preparation than the rest of the area where you applied the top coats. The different sheen that you see is probably mostly due to how light reflects off the wall in that area. 

One fix that may be possible, particularly if you had painted with a egg shell or low luster type paint, is to repaint with a flat paint.