What this means is you have a polygon on top of a polygon, this happens when you select the extrude tool and do not extrude but insted deselect it.
If you right click on your object and select face you should be able to see duplicate faces because there will be a face center dot located on the edges around the problem polygon/polygons.
Obviously you need to delete one of the faces and there is no automatic way to this so i'm afraid you will have to go in manually.