Check, that these pads/via aren't placed over other via which coordinates are coincide.
If the problem will continue, please send the design file(.dip) to our technical support:
support at diptrace.com
Now you can only edit BOM file in the text editor.
But the similar feature already developed.
You will be able to delete the some components from BOM list before exporting.
It will be available in the next update.