Having the total tax as $0 is a good thing. It seems that the standard deduction (or itemized deduction) and nonrefundable credits lowered your total tax to $0. The standard deduction increases each year. No, it won't get flagged if your total tax is $0.
Generally, your total tax cannot be lower than $0. But you might get more back than you paid in if you qualify for refundable credits.
Please see What Is the Difference Between a Refundable and a Nonrefundable Credit? for additional information.
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