When I completed my return, TurboTax asked if I had work done on a rental property that required a 1099. My answer was Yes. It was followed by a question that asked if I had submitted the 1099. I had not submitted it yet, so I answered No. It never walked me through the process of submitting the 1099, so I later followed a separate process to file the 1099. However, on my actual return there is a question that asked if I will be submitting a 1099 and Turbo Tax filled that in as a No. Now there is inconsistency with what was filed. Should I submit an amended return for this question, even though it does not change any numbers? I am concerned that it looks like I am refusing to submit a 1099 even though I submitted one.
I would not file an amended return. When you filed (or will file) the 1096 and the IRS copy of the 1099 they will know you have filed it. If you receive a letter from the IRS, just write back and explain just as you did in your question. They could assess you a penalty, but I I doubt they would for one 1099. If a business submits Form 1099 within 30 days from the due date, the penalty is $30 per form. If you file the form more than 30 days late but before Aug. 1, the penalty is $60 per form. The penalty increases to $100 for any form filed after Aug. 1 or not filed at all.
Filing an amended return won't change the fact that you filed the 1099-MISC late.