How to fix the via problem ?

I am a self learner trying to duplicate  the reference design from scratch.

Following is the reference design board file via pattern (layer-2 GND plane):

Here, drill and pads of the vias are visible and the clearance with the ground plane is also achieved.

Below one is my PCB design. Here two difference I have noted. First, I am not able to differentiate the drill and pads of the via. Undesirable connections of all vias and mechanical pins to the ground layer is second. Any advice to avoid this situation?

Tool: 17.2

Close up views of vias (layer 2 GND)

Regards,

VT