Smart Check is flagging EIN/SSN for rental income from tenant, but I don't have it. How do I bypass?

Are you trying to report that income as if you got a 1099-Misc?  Delete that and answer that no 1099-Misc was received, and then you can just enter the rent amount paid to you. 

Thank you - which form should be used instead, and under what subsection in Wages & Income that would be found under? 

In the Rental section for Income, select Cash, checks, and electronic payments (like Square or PayPal) and enter the amount you received.  @danielyzhou1992