2019 Excess Contribution

I am in the process of resolving an errant HSA excess contribution on my 2019 Tax return already submitted.  Current filing shows a $13,200 excess contribution with a $4800 Tax free employer contribution along with a $4200 deduction (not sure why this is the case).   When I amend the excess contribution by removing the $13,200, the deduction is eliminated causing income to increase by $4200 resulting in an increase to my tax burden.  this does not make sense since the excess contributions are taxed at 6%, my expectation is that the tax burden would go down.  Furthermore, can you explain why there is a $4200 deduction for the situation I described above since this is the cause of increased income?