Yes, it happens to me every once in a while,
Rebuild does put it back. I have not narrowed it down yet what is causing it.
SW 2012 sp2.0
It is/was happing to one of my assemblies. I think I stopped it but I am still testing it out.
It could of been happening due to what I was doing but I am not 100% sure.
Edit a part, offset faces (0.0) from a maiting part. I broke the external references and as of now it has not happened.
The blue faces are the offset surfaces from another part.
copy faces.png 105.1 KB