How do I fix my tax form showing an excessive IRA contribution when it is a negative contribution?

In 2021, I paid a $50 check to my IRA holding Co.  I included the maintenance fee voucher from the statement stating I owed $50. The IRA holding Co. deposited this check as a deposit into my IRA account.  This week, I called the Co. and asked them why I received a 5498 Form that indicated I made a $50 contribution on line 1.  The Co. counted my maintenance fee as a deposit and that caused me to have an excessive contribution of $50.  I am retired and had no 2021 income either.  They have allowed me to withdraw $48 because the $50 deposit had a loss of $2.  On the Turbo Tax program, I entered the $50 excess contribution and the withdrawal of $48.  Now the program and tax form show I have a $2 excessive IRA contribution.  What would happen if I over-ride the $2 and make it a -$2.  Can this be done?  How do I fix this?  Thanks.