Has anyone ever dealt with this issue and/or know how to correct this?

I have a fluid model (most info is proprietary) and it properly shows the fluid subdomain I created but it stops it short of the lid.  The features sizes in my model are very small.  Lid is ~27um x ~27um x ~505um long to cover the 25x25x500 slot outlet.  There is a hidden body I use for meshing but it has been omitted from the 'component control' menu.  Either way, the hidden body is not an issue because the subdomain is not stopping at the hidden body.  When I set BCs to the top surface of the lid, which should be in the subdomain, it gives me an error that faces are not contacting fluid region.