I am a pastor at my church but social security and medicare taxes are withheld from my pay. Should I check the box for 'religious employment?

If you do not have any other special tax situations (the most common is the parsonage), you do not have to check the box for religious employment- it is just a great feature in TurboTax that will add additional questions to get you the best tax results.

You are not being treated as a "religious" worker; basically, your church is doing it wrong and is reporting your wages as a secular worker.

If you have a non-taxable housing allowance (or live in a church-owned parsonage) this has the potential to screw up your taxes, and we need to discuss further.  If you don't have a housing allowance or parsonage, then you can just file as a regular W-2 employee and not worry about the special rules for clergy.  (But, the housing allowance is an amazing tax break and you should be taking advantage of it.)

Your church could correct this for 2022 but the paperwork is complicated, especially if its a small church that doesn't have other employees. 

Your treasurer or payroll person really needs to get educated and fix this for 2023.