Will e-filing be messed up if the control number/panel D is incorrect? I was told it is optional but when I go to file it says it is the wrong code for e-filing.

The control number in box d is not required by the IRS - it is used by your employer. As a result, if it causing you trouble, just delete it. If it is not causing you trouble, then leave it in - it won't matter.

You will need to go back and edit the W-2.  Remove the control number that is entered in box d of the W-2.  If the program throws up an error for this then delete the W-2 and re-enter manually leaving off the control number as it is not needed to e-file the tax return.