I remember last year with my NSERC rejection being quite bitter that a colleague got a PGS-D and didnt even publish a single paper prior to submitting her ap. I had at least 2 at the time. But what Ive come to realize and especially from others experinces is that there are many issues that can come into play in the selection process.
Heck even the criteria for getting your app outside of the university is vague university to university. Some universities have a criteria of grades only and do not look at all at any of your other accomplishments. So if the cut off was 92% regardless of your publications an 85 or 86 would get you a rejection in November at some Universities without the pleasure of a rejection letter from nserc. I know alot of guys doing research right now who have 70~80% averages that are far more canny at research and publishing than people with 95s but they cant break the university screen. I dont know why your app didnt go through at NSERC. But some years i would have relished the oppertunity just for my ap to have gone through the university screen. Could be a number of things why it didnt pan out. There is no exact sceince to scholarship acceptances/rejections its subjective based on some 30/50/20 scale for the reviewer who has multiple apps to go through and little time to do so based on many reasons listed here. I know of people with multiple publications and 99% averages still being rejected for scholarships (and being quite upset over it too).
The key is, rejection happens, and you need to make them make you stronger. Take it from somone whose been rejected 3x by Nserc, 2x by OGS, 1x by commonwealth, multiplex by some pretstigious University scholarship that i cant remeber and use this motivation; Prove to them why they made a mistake by publishing even more and excelling in your research. Theres other scholarships out there that are more prestigious go for them. But always keep in mind that no matter how great you are or think you are. Scholarships and grants are hit and misses. You win some, you lose some, and you keep at it;) Thats academia. BTW my grammar and typing is atrocious here, but this is not an app for nserc thankfully