I have the same issue (and have, for years). I finally asked my VAR about this. This was their official response:
"From my experience, doing mirrored parts doesn't very often copy the correct hole callout information unfortunately."
I cannot believe that after decades of improvements they still haven't fixed this very basic problem!
It works in SW2017 (it will also double the quantity). If you are not running that then you need to use a circular or linear pattern. I would need to see you model to tell you if that is feasible.