Stuff happens. I often have seen these kind of tolerance issues, even in flight hardware for space.
You can easily maintain these kind of tolerances mechanically, but if there is an error in the technical drawing package, you will mill the part to the wrong tolerance and you will not catch it in inspection.
For instance if the designer writes down the wrong clearance fit, or the wrong reference plane to the clearance then you are lost, no matter how accurately you can work.
Should not happen, but it is humans doing the job.