It appears so .. personally I would not have imagined someone getting a rejection based on NOC code but there is a case like that .. so yes that is a possibility.
In your case, if I were in your situation (my personal opinion.. you can disregard), I would choose the NOC which is closest to my education.
So, if you are saying there is hardly any difference between civil engineer NOC vs Mechanical engineer NOC .. I would choose Civil Engineer if my education is in that field or vice versa. Although, NOC is NOT education dependent and only job duties matter .. but I think I would have used education as the tie breaker question