I had 2 1099-R's issued in 2018. Both were offset by 5498's as I repaid both IRA withdrawals within the 60 day period & entered 5498's for both. Why a 6% penalty?

[SweetieJean]

You are only permitted to make one IRA withdrawal/repayment every 365 days.

[dmertz]

TurboTax does not enforce the one-rollover-per-12-months limitation.  TurboTax indicating a 6% penalty implies that you entered a new IRA contribution under Deductions & Credits that you were not eligible to make.

As for rolling over a distribution made within the one-year period following the date of another distribution that was rolled over, this is indeed results in an excess contribution (to the extent that it exceeds the amount you can deposit as a new contribution) as SweetieJean indicated even though TurboTax does not report it as such.  An excess contribution is subject to penalty each year it remains in the account and there is usually no statute of limitations on how far in the future the IRS can assess those penalties, should the IRS ever detect the violation.