Accidently was categorized as Tax Exempt for 2020

I some how was categorized as tax exempt from Feb-Dec for just my federal taxes at work. I have already contacted them and there is nothing I can do to change it at this point. I am fully ready to pay the amount I will owe but do I just file like I normally do? Is there any penalty for not having the contributions come out in 2020? Please let me know anything I should be aware of in this situation.