Senthi, the NTA score in the official score card refers to your percentile and not your actual marks scored. The actual marks are not officially declared by NTA since they have been normalised accordingly to equate the difficulty level of the question papers throughout all the shifts and days of exams.

So now percentile is your relative performance with respect to the other appearing candidates. If you get X percentile, it means that your performance was better than X% of the total candidates. It is calculated separately for the individual subjects as well as the overall paper.

So the total NTA score or percentile is independent of the NTA scores or percentile in the different subjects. It is your relative performance in that particular subject or paper with respect to others. That is why it is possible that your overall score is less than the individual scores since score, here, refers to percentile.