No, they are individually marked.  He had some exceptions to the 10 penalty on his, and she did not.  So his was included in the e-file, and hers was not.  I know that if you only owe the 10% with no exceptions, sometimes the software does not require the 5329.  But here is a couple, one who has an exception and one who does not.  The 1040 says "No" for requiring the 5329, but the 5329-T was included, which is where the IRS is having an issue.  I could split the exceptions between the two of them, which would make both generate, but the problem is the return has already been filed and the IRS is now saying that they owe less than they actually do because the 5329-S is not there to support the number on Schedule 2 and the 1040. The client feels that I did something wrong and they owe less than they actually do.