FedEx marked one of my packages as delivered but it didn't show up until 6 days later (the replacement arrived on the same day...). I assume someone just forgot about it on the truck, since the other one was actually delivered on time.
I've had far more problems with FedEx than with the contractors who deliver Prime Now.
FedEx (unlike UPS) routinely delivers packages a day late, and they often leave packages in front of my garage door (where they can get rained on) with no notification.
I've found that the way they honor this guarantee is that you simply return it for the reason "Did not arrive on time" and you get a refund.
I've done it once because it didn't arrive on Friday, wouldn't come until Monday, and I wanted it for that weekend so I just went out and bought it and returned what Amazon delivered Monday. I felt kinda guilty but when it came Monday it looked like it was run over by a truck anyways, as in, had actual tire tracks on it.
Amazon hasn't honored the two day guarantee for me in these instances.