I just dealt with a 12C notice today that made no sense - said the W-2s submitted with the return (which was e-filed) were not sufficient to support the excess SS tax withheld reported...that Lacerte automatically calculated correctly...they wanted me to resend the W-2s. 

So, I also say yes - maybe the IRS' software is just as screwed up as ours were this tax season. 🙂