Why does vertex merging cause non manifold geometry? I am having issues with some non-manifold geometry.. I understand there are a few types or a few sources of non-manifold geometry, but I can't find the exact issue with my model..
I noticed most of it, if not all, was located where I merged vertices together. Why would this cause non-manifold geometry? I thought the goal of the merging process was precisely to make sure I had a unified mesh?
Here is the file in question, maybe I missed something:
Your mesh contains flipped faces, which is considered non-manifold geometry.
It's probably not caused by merging vertices, and it's easy to repair

Select all faces
Go Mesh &gt; Normals &gt; Recalculate Outside
Done.

After this, there are still some non-manifold vertices on the outer rim, because the mesh isn't 'closed'.