It's just the forces of the trains. When it's not a derailment it's breaking them. They're doubling the running room for slack action^, for one. That's the least of the concern, but there's more potential for breakage because there's more potential for greater differences in velocity from one end of the train to the other. Topology also matters, previously consists here average 135 cars, but range from 115 to 150, they're 53' each. Usually they'll have 4-5 motors at 74' each. Suffice it to say, depending on the territory there can be huge force differentials generated which can break trains or rail, think cresting a grade on undulating hills. And you can "stringline" trains too, literally pull cars off the tracks, and it's exactly those forces that'd do it.
And then there's the human element. Nobody knows when they're going to work, how long it's going to take, what kind of bullshit they're going to run into. You can get stuck for long periods of time away from home terminal, and the Class 1 doesn't care. And there's things like rules on how to walk. The environment that's been constructed isn't meant for human consumption and it's taking a toll on the workforce. There's reams of other shit to whinge about.
And the derailments always matter, it's a total clusterfuck. They're not easy to fix, you've got to "bad order" and set out the car, at least by regulation. This involves rerailing, finding a set-out track, and making all the moves to get everything back in order. You've also got to wait for carmen (who are understaffed) and management, which depending on the route, could be a long sit. If it's bad enough it'll shut down traffic for a couple of days, requiring significant diversions around it while the Class 1 pays out the ass for a third party to come clean it all up and rerail shit.
None of the current infrastructure is built to deal with these train lengths, either, so everything moves slower. The fact the Surface Transportation Board had a hearing with the Class 1's, I think, is a pretty good indicator they're about as interested in moving goods as GE is in manufacturing.
^: Each coal car has two draw bars with +/- 2-3" about the same for shipping container cars (from eyeing it) of run built in. This varies with car, auto racks have way more run out. Opposing forces in the trainline will pull it apart, the more run to build the faster the opponent acceleration... This typically results in broken knuckles. But it is possible to just push cars off the rail with these forces, which is exacerbated by the doubled length.