volker_muehlhaus can answer better than me but I think there is an port definition error.The ports are normally simple ports and they don't have any extension to the lower layer.
If you post your projetc file, we can answer better.
Remove the vias at the port. Sonnet box wall ports are grounded to the box side wall. There is no need to draw a ground via, because the box wall already creates that ground connection.
Independent of this port problem: For the via, you can draw a cover metal manually, or switch on "via pads" in the via properties.