I have had one that has been a huge ordeal over the last few years. Client came to me with three years old returns due. Wife is a realtor with 1099 income (substantial expenses with commissions, mileage, etc) and husband with retirement and misc side job income.
I file a joint tax return for 2002, 2003, 2004 and 2005. (This takes a while, as client has to get all records together) IRS does not seem to see the returns, despite payments that were enclosed and that they deposited. IRS leaves husband alone and "prepares" a single return for wife on 100% of her 1099 income for two of the years. This has been the biggest mess I have ever had to clear up. I would send letters, I would speak to IRS agents and it was supposed to be all cleared up. Then another letter (based on the wife's single return) would come about the tens of thousands of tax dollars my client owed. I would recommend that you include cover letters with the tax return explaining the sequence of events with the new returns you are filing. Not that they will read the letter, but when you are trying to clear up the problems that may follow, at least you can refer to that letter.
By the way, with my client, we finally ended up with an OIC and the IRS agent that was working with us on the OIC was finally able to stop the collection letters on the "single" tax return generated by the IRS. After lots of back and forth, we thought the OIC was accepted in early June. On Friday, I had a message that IRS agent needed to talk to me one more time! Last discussion I had before that was that we would be getting a letter with acceptable terms!
