My accountant filed my personal tax return this year on-time but he filed a automatic 6 month extension for my s corp. He was suppose to file it on April 11, 2013 but instead he forgot and filed it last year. Since the personal tax return has my data from K-1 but it was not filed when the personal tax return was filed, won't there be a mismatch and IRS will look at it because my s corp was filed later than the personal tax return?
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No. It may delay the processing of your personal return, more so if you're claiming large pass through losses or credits, but it won't generate an audit of either return.
Yes, there will be a mismatch. The income reported on the K-1 will not be reflected in your 1040 tax return, and in a few months the IRS computers will detect this and you will receive a notice from the IRS requesting the payment plus interest and penalty. So you should file an amended return now and pay the additional tax along with the filing of the S corp tax return -- in order to avoid additional penalty/interest.
But if the 1120-S has a loss on it, then I'm not sure if the IRS will calculate a notice giving you a refund. You should also file an amended 1040-X showing the negative income on Schedule E, along with other items such as charitable deductions if any, and you will get a refund check from the IRS that includes interest.
So either way, you need to file a 1040-X. Don't forget the amended state return as well.
What the tax preparer should have done is estimate income from the S corp, file an extension of your personal return and pay the estimated amount due along with the form, and then file the 1120-S on time, and then file the 1040.
As the 1120-S was late, I think there is a late penalty of at least $90. Your individiaul federal and state returns will also have itnerest and penalty. Perhaps your tax preparer should pay these.
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