Given the case of Suaad Hagi Mohamud and Abdihakim Mohamed, and perhaps others, mistakenly imprisoned over apparently suspect passport photos, I wonder if part of the issue is legitimately related to the photos themselves.
I've held three Canadian passports, the first two of which were the type where an actual photograph was laminated to the page. The photos in these two passports are bright and clear. Indeed I had one set of photos rejected because there was the faintest line of shadow under my chin - the rest of the photo was crystal. Given the passport office queue started before 7am, and I had to make a special trip to Toronto for it, and the official behind the counter was full of attitude, this was just annoying.
Current passports appear to print the image directly on the page. My latest one came back with an image so dark, I can barely make out my own features. When I saw it, I was actually concerned that I'd have problems travelling with it. I can only imagine how someone of a darker complexion would appear. However, it seemed to satisfy the Passport Office, (or passport office computer) enough to send it to me.
If this is the case, it would make sense that a KLM staff member or customs officer might be cautious. It would also come as no surprise to find out that this government would rather bugger brown Canadians with non-western European names than admit an expensive problem with our state of the art super secure passports.