Also bear in mind the controller converts circles and arcs to line segments when cutting with the tolerance controlled by the max deviation setting. Also some post processors will not output G2 and G3 but will instead output line segments with their own tolerances. This could also lead to under or oversized holes. When I created my dog holes I had the same problem, the dowel pins I had did not fit. Using Fusion 360 I used a negative stock to leave value on my toolpath increasing the value by -0.01mm until the dowel pins fit properly. This is not an ideal long term solution for all projects but might make sense for ones requiring greater accuracy.
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