Run the check sequence.
I found multiple problems with your layout even before I ran check sequence.
The problem you're having with the faces is on multiple levels.
You have problems with your face definitions as well as overlapping channels between the faces.
I was able to clean it up and make it work properly in a very short time but like I said in an earlier post I have absolutely no idea how you plan on wiring anything.
When I ran check sequence I saw probably the largest list of overlapping channels of any layout that I've checked before and without knowing how you plan to wire it I wouldn't even know where to begin to straighten it out.
I would suggest that you first work on all of the overlapping channels and get those cleared out then look at the face definitions.
