The only time I had a problem was when I had confirmed upgrades but had changed through central reservations my routing from YOW-YYZ-YYC to YOW-YEG-YYC. The machine spit out my boarding passes for YOW-YYZ and YYZ-YYC still instead of YOW-YEG and YEG-YYC. The gate agents took them mistakenly and it caused a little hiccup in getting proper credit. A letter to Air Canada resolved the situation quickly. I was surprised that the gate agents didn't catch the mistake.