Dave and Box have already pointed out two of the key techniques. Set the model units to the max possible before using the text tool to label vertices. Drawing diagonals across faces that won’t form is also useful for tracking down gaps and isolated off-plane points in the boundary. Always turn on view->hidden geometry while hunting.
Beyond that, it’s mainly a matter of experience, of knowing what sort of things to look for and how to search them out. In this case the error (a couple mm) was larger than usual, which is why I was embarrassed that I missed it - often they are smaller, sometimes so small that you wonder why they caused any problem!