Just had this issue today and like a number of you, TurboTax decided I might owe a penalty. I filled out the waiver, but I was uncomfortable with that as a solution.
Situation - two IRAs and total RMD was what was required. But I took more out of one IRA and less out of another. IRS Pub 590-B, page 12 specifically allows this.
Fix - when TurboTax asks for the RMD in the account where you took out less than what your brokerage firm stated the RMD should be, DO NOT enter what is on your year-end statement, enter the amount of the RMD taken as the required RMD. On the IRA where you took out more, do the same - enter the amount you actually took and not what your IRA statement showed.
Caveat - supposes that all RMDs taken do in fact total to at least the RMDs required.
