Yes, you have to file a Form 1040X amended return because the IRS does not know about your expenses. They see only the additional unreported income on the 1099-MISC.
You are required to keep your own records of your self-employment income and expenses, and report all of the income and expenses on your tax return, whether or not you get a 1099-MISC. In the future, if you report all your income on your original tax return, based on your own records, it won't matter if a 1099-MISC is sent late, because you will have already reported the income (and associated expenses, if any).
