We held up the FP line one time at Toy Story Midway Mania because I had 100% made a fastpass and it showed up in my app, but our bands were getting the blue swirl of rejection. I felt really bad, but it also didn't seem fair that we should just leave and give up on our fastpass because of their technical issue (they did figure out I was right in the end, but it was super embarrassing and I'm sure everything thought I was just trying to sneak my way into the shorter queue).
But those are the kind of delays that add at most 5 minutes while they get figured out. For it to be a substantial wait like 45 minutes, I think what must be going on is rain or ride shutdown closures causing greater "anytime FP" usage.