Screenshots? Link to a public project?

The easiest way to deal with mounting holes is to either create your own or just chose one of the library symbols for mounting holes which have Footprints associated with them, place them in the schematic and then do Update PCB... Some of the symbols have a pin to connect a net such as ground to. If this is to be left unconnected, put a Not Connected green X symbol on it to avoid it giving an unconnected DRC error. An example is: HOLE\_D3M5\_D7M0\_PAD\_PTH which is an M3 clearance hole (3.5mm) with a 7mm diameter pad for clearance with all the slop in the screw and an M3 washer. This has a single pin. You may wish to edit the Footprint if necessary to suit screw and washer clearances or edit the symbol to remove the pin. After making changes to the PCB do SHIFT-B to rebuild any copper areas then run the DRC.

@andyfierman Thanks Andy :)