That's exactly how I did it. Initially with a 2d geometry that was extruded 1mm with one mesh element in the z direction. The interface zone for each geometry has many divisions, but they're all connected through SpaceClaim connection feature. SpaceClaim also indicates that there are no geometry errors. Could this possibly be a software issue? I will try to download an example problem for System Coupling and solve it.
I should also mention that my geometry is supposed to be a longitudinal section of a tube, so ideally I would be simulating a 2d geometry, but since System Coupling doesn't accept lines as data transfer regions, I made a small extrusion to get the areas for that.
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