I'd say its more likely it was an unusual event. Amtrak trains don't generally lose two hours out of nowhere from host railroad mismanagement- outside of UP territory, anyway.
What does happen is a train sits for 5-10 minutes for something (legitimate- a defect detector, for example), Chessie-Seaboard lets something pass it, and then CSX dumps it onto Norfolk Southern 30 minutes late. NS is not ready to accept the train outside of its assigned window, and the train runs in where they can fit it corresponding to the efficiency of the specific dispatcher, and it pulls in to Chicago 3 hours late. That's what you find as delays due to host mismanagement. Not the train sitting in a siding for 2 hours. Hosts get fined for that stuff these days.
When a train looses two hours on a single host between a single pair of stops, it's one of two things:
a) The train is on Union Pacific trackage.
b) Something went wrong.
What went wrong? An Amtrak mechanical failure (but unless it was given running repairs, this is not likely. Two hours isn't long enough for protect power to get to the train there from Albany or Buffalo), a freight derailment (although that information would be fairly easy to find if you bothered to look), a freight mechanical failure (this wouldn't get in the news the way a derailment would), a grade crossing incident (likely make the news), a bad ordered car (very possible, it could take two hours to figure out and accomplish how and where to cut out a BO in the middle of nowhere), or most likely of all, some kind of passenger incident.