State filing in VA and DC resulting in penalty

My daughter lives in VA and has two jobs.  One in VA and one in DC.  She received a W-2 for each job and both have federal and state withholding.

after paying $40 to download the DC tax form, I got started.  The first thing it said was that it recommended that I file the DC nonresident request for refund.  I went through the process and then proceeded to complete the VA tax return.  At the end, I noticed that it included a $29 penalty.  It appears that this is due to filing all her income, VA/DC combined, through VA, and since her VA withholding was low, she was penalized.

Did a step get missed somewhere on the VA return to indicate the nonresident refund for DC?

 

Or is better [or is there even an option] to file each State return separately even though she lives in VA?