Do people with above 99.90 percentile get rejected in IIFT Delhi? My GEM profile is pathetic and I am only targeting IIFT Delhi (and not IIFT Kolkata).

IIFT Delhi has rejected even 99.88–99.92 percentile candidates in the past. Candidates with 99.xx and 96.xx percentiles have similar entrance scores, but those who performed well have an advantage in the admission process. 

Do not be complacent in the GD, WAT, and PI rounds. Candidates with high percentiles have similar absolute scores, but the entrance exam score weighs 55% of the final composite score. So individuals with high admission exam scores have an advantage but might still be dismissed if they perform poorly in future stages.