Sometimes because of the freight railroads.
Sometimes because the passenger equipment breaks, or wasn't available. (One way that can work is, if the train is hours late arriving at the endpoint, that equipment isn't available to become the next train in the opposite direction.)
Sometimes because a passenger becomes ill, or even dies, or (as ars said) becomes unruly enough to need arresting.
Sometimes because some driver wasn't paying attention, and ran into the train (or into the freight train ahead of the passenger train).
Sometimes because of weather. (Two feet of snow since the last train passed can slow down a train significantly. Either too much heat or too much cold lowers the safe operating speed. Too much rain can cause problems, too.)
And so on, and so on. Sure, a lot of the time it's the fault of the freight railroad. A lot of the time it's not, too.