unlucky my friend...

Steve is right on one count and keep faces together MUST be ticked before extruding anything.

The other issue, and I have had this one personally, is you have faces on top of one another and all occuping the same space, this is caused by extruding incorrectly or not having keep faces together ticked.

The Clean Up action will not resolve it, it never will for this issue, so I must be the barer of bad news and say go back to on older version (get into the habbit of saving diff versions as u go), or start over again. No Tool will fix it and to test if you have the issue, select a face and delete, there will be another under it and so on until u get no faces left.

As I said Clean-Up will not fix it, I think this maybe due to merged verts, but multiple faces on the 4 vertices.

Sorry...