i am have issues with my solidworks part/feature. 

My issue: I have a solid extrude and then added a surface boundary on one side and then used the mirror function the mirror it to the other side. after some knitting and a shelling, I went about cut extruding a hole through the top of the combined Surface boundary/extrusion, but i am now having issues. after the cut extrude, a couple of faces have deformed, but only on the Original surface boundary. the mirrored boundary works, but the original doesnt. (this is my first shot at surface modeling so there might be a few issues. (One issue might be that i used the base flange to make then base instead of extruded boss base for some reason,