Deluxe Turbo Tax, after entering a 1099-R, it asks several screens later to confirm the RMD again which increases the taxes owed, is this correct? I had taxes deducted.

If you met your RMD for 2024 then you shouldn't have a penalty on Form 5329. Please review your answers. Sometimes it helps to delete and reenter Form 1099-R. 

If you have code D in box 7 then please see Why am I getting an error when entering Form 1099-R box 7 code 7D?

Please follow these steps in TurboTax Online:

1. Login to your TurboTax Account 
2. Click on "Search" on the top right and type “1099-R”
3. Click on “Jump to 1099-R” and enter your 1099-R
4. Continue until "How much of the $XXXXX was a RMD?" screen and select "The entire distribution was an RMD"  /or select "Only part of this distribution was a RMD" and enter the amount of RMD (if this distribution includes RMD for other IRA accounts then you included the amount here)
5. Enter the RMD amount for this account on the "Let's get more information about your Required Minimum Distribution (RMD)" screen
6. On the "Review your 1099-R info" screen click "Continue"
7. On the "Did You Miss a Required Distribution From Any Retirement Accounts?" screen select "None of these plans failed to withdraw the RMD" if you met all of your RMD for 2024, otherwise select what is applicable. 

In TurboTax Desktop:

1. Click on "Search" on the top right and type “1099-R”
2. Click on “Jump to 1099-R” and enter your 1099-R
3. On the "Required Minimum Distribution" screen enter RMD for this account 
4. On the "How much of This Distribution Applied to your December 31, 2024 RMD" select "The entire distribution applied…"  / or select "Some of this distribution…" and enter the RMD amount (if this distribution includes RMD for other IRA accounts then you included the amount here)
5. On the "Your 1099-R Entries" screen click "Continue"
6. On the "Did You Miss a Required Distribution From Any Retirement Accounts?" screen select "None of these plans failed to withdraw the RMD" if you met all of your RMD for 2024, otherwise select what is applicable. 

If you have multiple IRAs but took the total RMD only from one IRA then select "An IRA..." on the "Did You Miss a Required Distribution From Any Retirement Accounts?" screen select "An IRA..." and click "Continue". On the "Total RMD for all other IRAs" screen enter the RMD from your other IRAs (where you didn't take a distribution from).

Please see Can an account owner just take a RMD from one account for additional information.

You are not required to file Form 5329 if you met all of your RMD. TurboTax will enter the information in the "Additional Retirement Account Smart Worksheet" to check that you met the RMD but this will not be sent to the IRS.