In the certification screen for the bowler in question, there is a small box "Card Group". In that, where you might have the radio button "Standard" selected, you should instead select "Additional".
With that done, to the right, the box "USBC Certifications" has a series of checkboxes. You should then be able to select "Local Dues (BA)" or possibly "Local Dues (WBA)".
This is not a discount per se. Your local association may (as an example only) offer a senior discount, which would be where the local dues might be, say, a dollar or two less, but some fee would still be required for the bowler.
Always check, download, and install the most recent update of your software to ensure that issues may have been corrected.