You are responsible for double checking your own tax return.
When entering a W-2 for clergy wages, there is a page listing special circumstances, and you must check the box for religious wages. You will then be presented with a screen asking you to enter your housing allowance or value of your parsonage, and you will be asked if you want to pay SE tax on your wages only, housing allowance only, both or neither. Both is almost always the correct answer. Wages only and housing only should only be used if you have a non-standard W-2 from your church, and "neither" is only used if you have an approved religious exemption to SE tax under form 4361.
Did you check the box for religious wages when preparing your prior tax returns? How did you answer the question about SE taxes?
In general, the way to fix the problem is to file amended returns and pay the back taxes you will owe when your taxes are recalculated. In most cases, you will only need to amend your federal return, your state returns should not have been affected.
https://turbotax.intuit.com/tax-tips/amend-return/how-to-file-an-amended-return-with-the-irs/L6kO691...
https://ttlc.intuit.com/turbotax-support/en-us/help-article/tax-return/amend-federal-tax-return-curr...
