It has a lot to do with the extrusion multiplier, the speed and nozzle size of your printer. I'd start by using a 0.4mm nozzle or smaller. Verify your extrusion multiplier is set correctly. If all is correct, I wouldn't know why your hole gets printed that size and I'd suggest just drilling it out. The main thing is there is material to drill into, the original model accommodated a 3mm shaft and I could get it to fit my 2mm shaft motor.