In the Form 1040 instructions, it says to put «NRA» in the space for SSN for the other spouse if they don't have one when filing separately. (money.stackexchange.com)
It comes into play when banks use SSN as a means of identification, or when they're required to collect tax ids (for interest bearing accounts). (money.stackexchange.com)
It means that you went in to access your refund using the Secondary SSN on the return and you flagged now as potentially being identity theft. (thecollegeinvestor.com)