Don't sweat it. Nothings wrong. The dot just appears at the center of the vertices of that make up the face. So when a face is nonplanar (as most faces seem to end up being) the dot can 'dissappear'. But its not really gone. Its just hiding from you on the other side of the face. Using the Xray mode helps in this situation or I've also found moving the camera back helps too.

Hope this helps


Dave