This video shows the issue I have... I am trying to extrude to add not remove an extrusion. But, I am showing an explanation point. These boxes are in increments, to your left to right sets goes up in elevation. I've tried to shift, ordered no luck.
Solved! Go to Solution.
The error that keeps popping up (non-manifold) is a result of your new solid just touching another existing solid at a boundary where they neither share material nor are the separated by any space (thus the zero thicknes).
Ken is right about the cause of the exclamation point error. To work around the error, you can use a symmetrical end condition, or extrude a short distance in the other direction as well. Let us know if that works for you.
,<edit> Matt's solution of going multibody should also work.