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It would not have been flagged as it's not considered a name change to not use your middle name on your documents. Just make sure your DS-260 and ACRO police certificate lists your full name (with middle name) in the section for other names. On the DS-260 field for Name, you must enter your name as it appears on your passport. So "SMITH, JOHN" only. Then enter "SMITH, JOHN ADAM" in Other Name(s).
Note that your visa (and green card and SSN card) will list whatever name is on your passport. So unless you get a new passport with your middle name listed before the interview, your visa and US IDs will not list your middle name either. This is ok in the US, as many Americans don't use their middle names on their IDs.