This is a natural consequence of using a non-full-thickness mold, unless you are very careful with bending, fitting and gluing of ribs. With a bit of practice you can learn to "tune" your technique to achieve the degree of wonkiness you desire. A certain degree of asymmetry can make things look more interesting. For perfect perpendicularity you need to get the ribs fitting very well to the form (I can see some quite large gaps in your photo), and glued up so that the rib is straight (ie rib edge parallel to the end block and equal "overlap" with each corner block....).
I don't think it's anything to do with your flattening process.