I think you may need to "compound" the holes into the main part of the decal so it knows it is cut out of it. Otherwise Flexi thinks you are printing that as just a circle. Or you can just select the "hole" and add the contour cut to it, then group all together. Essentially if the hole is actually a hole you should see the artboard through that area. You can change the color of the artboard to confirm that it is actually a hole as you will see through that area.