If you are using Ultimaker Cura 4.4.1 slicer you can change the tolerance of holes by doing the following.
Click on preferences /Configure Cura, In the window that comes up click settings. On the top right hand side pick Custom selection from the drop down menu. Then Settings from the list on the Left. Scroll down to Walls and continue to near the end of the Wall section and tick the boxes for Horizontal Expansion and Hole Horizontal Expansion. This will show you these options in the print settings menu you get when you are preparing to print. You have to save these settings and pick it from the Profile drop down to use it. I have only needed to use the Hole Horizontal Expansion. With my printer I find that a setting of 0.25 works for most of the metric holes and threads I use.