If your W-2 is incorrect concerning the 401(k) deferrals you need to speak to your employer's payroll department to get a corrected W-2.
And no you do not put the difference as an IRA contribution.

The code D is for 401K contributions but did you also do 401K ROTH contributions ?  Do you have a code AA in box 12 with the missing amount ?

"section D"'  You mean W-2 Box 12, code D?

NO ... never.  Have the employer correct the W-2.