Polygonal Plates Improperly Connected

I created my model with two holes through plates. I achieved this by polygonally meshing the plates and creating a hole simultaneously.  Then I needed to mesh all other connecting plates. Now I am getting warnings that  my plates are improperly connected and that some plates are warped or not shaped well.  Is there any way to create a round hole and mesh the plates so that they are properly connected?  I have attached two photos.