Read the CP2000 notice carefully ... they should have taken the withholding into consideration. This error may have triggered other things on the return like more of SS benefits being taxable and/or credits being disallowed.
If the IRS is correct you really don't have anything to contest ... you missed it so just sign the form agreeing to the error and send them what you can asap. If you fail to send in the entire amount then the IRS will send you a bill for the balance + penalty + interest. The faster you pay it off the cheaper it will be in the long run.
