The fan case has an inside radius of 4.4mm. If your fan body has an outside radius much tighter than that (2mm in my case) the fan doesn't seat on the edge. This causes the hole pattern to be misaligned.
This is a simple remix to make the radius 1.5mm up most of the height of the case. It transitions back to the original radius so the carbon section still fits as expected. A small chamfer removes the need for supports on the overhang.
The author remixed this model.