i have 3 iras and took more than required total rmd amounts across all 3 but turbo tax is still calculating a penalty

The IRS does not know the actual amount of required minimum distribution (RMD) for one account or all accounts. If you have taken the full amount of your RMD for the year, then you should indicate when asked for each account 'How much of the $___ was an RMD?', indicate the entire distribution was an RMD. This will eliminate the penalty.