I had this same problem and was baffled. Here's my best explanation of the solution:
You'll notice a small groove on the arced edge of the aluminum body of the Mac Mini where it meets the wi-fi plate. The perforated part of the plate rests above/within this groove. I noticed that if you push the plate into place and use a hook tool hooked through a perforation hole in the plate along the edge and pull up, it rests properly. You may need to do this little by little throughout the arc of the plate as you're pushing the plate into place. Eventually it will seat correctly.