I assume that you mean that it's a Form 1099-R.
As you discovered, a Form 1099-R that includes code B in box 7 is not permitted to have the IRA/SEP/SIMPLE box marked because code B means that the distribution is not from any kind of IRA. You should try to escalate this with the payer to obtain a corrected form.
It's impossible to guess from the limited information provided if the marking of the IRA/SEP/SIMPLE box is incorrect or if the code in box 7 is incorrect. It depends on the type of account from which the distribution was made. It seems more likely that they just marked the IRA/SEP/SIMPLE box inappropriately and the distribution is actually from a designated Roth account in a 401(k), 403(b), 457(b), and account that is not an IRA.
If you are unable to obtain a corrected form from the payer, the correct action would be to submit a substitute Form 1099-R with the appropriate correction, but doing so will prevent e-filing.
Is the Form 1099-R from a bank or from an employer-provided retirement plan?
