Not necessarily. Nothing in the OP indicates that the 12th player was in the huddle an inordinate amount of time. This is clearly a foul in NCAA, but there is not a FED rule that says breaking the huddle with 12 is illegal.
What IS illegal is the sub not coming off "immediately". There IS judgement that comes into play when deciding what "immediately" means, and if there is no A) intent to deceive or B) actual deception (even if unintentional), you have no reason to flag this other than showing that your are an OOO.