ok heres what you do ..under the Mesh menu select Cleanup and in the option box that appears look under cleanup effect and check mark Select matching Polygons then a little lower under remove geometry check mark Nonmanifolder geometry then hit apply.Your mesh should now have the nonmanifold geo highlighted (it might hightlight faces or vertices but now you know where the problem is. there are a few reasons for these components to be nonmanifold so you will have to check them out , some things that might be wrong include duplicate faces on top of one another , unmerged vertices or maybe face normals reversed.
If you can't identify the problem then a quick solution is to delete the offending faces and use the append tool or the bridge tool to replace them.