Also had this issue. I think as a newbie, there may have been times when the wrong key was pressed (or with/without pressing CTRL / Shift etc). For example, there’s object mode and edit mode.
If you press Shift+D to duplicate in edit mode when you should be in object mode, then I think a mess is being made to the mesh! Lots of duplicate polys.
What spikeyxxx said is interesting… Blender really should have an option on the extrude tool to not create all those inside faces. To try to fix those is a nightmare for me just trying to select them! Kent’s solution was, unfortunately, never going to work! For me hhaase has the solution other than just creating the main box again.
However, trying to create the main box again, I came across a Blender issue. Trying to do those loop cuts with the mouse is so difficult! I found mouse accuracy while trying to snap can also be a problem. Maybe this is all new to 2.8a which I’m using.
