Micro USB Type B Receptacle Mounting Holes Near Pads
I've seen a couple of USB connectors with plastic alignment pins in a similar place. However they are usually slightly further from the pads. If your connector has alignment pins and you don't place the holes, the connector won't fit. 

My suggestion is the same as for any component - don't trust that the footprint you have found is correct/accurate - most won't be. 

Always verify the footprint against the manufacturers datasheet for the connector you are using. Make any changes as required.