A Control Number (box D) is used by many payroll departments to uniquely identify a W-2 in their system. If your W-2 doesn't have one, it's no big deal.
If you get errors when attempting to e-file with an empty box D, just enter any number in this format: 5 digits, space, 5 digits (for example, 12345 67890). The IRS doesn't care what's in box D.
If you get errors when attempting to import your W-2 with an empty box D, select Skip import and manually enter your W-2.