patchy patches
 

I'm trying to use SnappyHexMesh to create my various patches. They come out, well, patchy. Can anyone shed some light on what causes this?

I have no idea what that image is showing. Can you add more meaningful images, e.g. what should it look like, what it looks like (with an explanation what is plotted there?). This seems to be a points representation, the Menu says Surfaces With Edges but its probably from another node.

Patchy Patches
 

Thanks for pointing out that my question isn't clear.

I've attached a rendered stl of the domain. Patches: Inlet: red. Outlet: green. Supplementary inlets: Y+ end of the elliptical tubes.

Those two patchy rectangular shapes from my original post are the inlet and outlet patches. At that scale, the supplementary inlets don't render. There are only a couple of remaining faces.

In this case I modeled the domain and imported as .stl(s). I've tried the other way and modeled the bodies, using patches in blockMesh. This works well for the two patches that are coincident with blockMesh faces, but I've been unsuccessful in getting SHM, or any other method in a decomposed case, to create the other inlet patches.