I would first make sure you are entering the form in the correct spot. Usually, only W-2s have control numbers.
However, if you are entering your 1099 and it is requesting a control number, you can just leave it blank or just enter any number in this format: 5 digits, space, 5 digits (for example, 12345 67890).
A Control Number (Box D) is used by many payroll departments to uniquely identify a form in their system. If your form doesn't have one, it's no big deal – you can simply leave it blank.