I added some m3 mounting holes and then when I try to run the freerouting tools I get this error:
How can I fix it?
Add them to the schematic?
You’d probably get errors for DRC too, attaching footprints that aren’t annotated to GND. I account for mounting holes in the schematic. There are symbols for them.
To KiCad, a mounting hole is a component. I put mine together on the font page of hierarchical schematics.
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I should. What is the part name? or I can just add a pad?
Edit: mounting pad
Search for “mount” and you will get a number of choices.
Then you can just link the symbol to your desired footprint.
Don’t know what size you have set for your M3 mounting hole, but I defined mine to be 3.5mm. This not only allows space for slight mistakes in the mounting screw positions, it also makes sure there’s plenty of space after the hole is plated.
Thanks. is this also because I should consider the nuts size?
You always need to account for the head or washer size of your mounting screws- make sure it clears components on the board.
My mounting holed have 7mmx7mm pads (square with rounded corners.
Typically, I drill a hole in my case, then fit a shakeproof washer and nut. Then fit the pcb, another shakeproof and another nut. The large hole gives me plenty of “drilling error”, and the large pad means the nuts won’t short anything.
Depending on your design, you may want the mounting hole to be isolated or connected to gnd / 0v.
PCB hole diameter is specified for after plating, not the drill size. You should never have to make this allowance.
Agreed, but mistakes can happen.
I just measured the 3.5mm holes on my pcb: 3.6mm!
Not only mounting holes, but I am also putting ground symbols on the schematic as (I will call them components) that show up on the pcb. I guess I could have just drawn and replicated them on the pcb but mine are symbols>footprints which appear only on the front silkscreen layer.
I guess that doing this allows me to grab it from the library instead of having to create it or copy it from a different project.
Does this make sense? A symbolic victory or ground to a halt? 
Depends on the pcb house. Where I work we use two different places and it’s weird because the one that makes the better quality pcb does not account for plating thickness in holes.
Most PCB fabs don’t tell you the drill sizes that they use, metric vs imperial gives them some options.