Which doesn't seem like a particular issr with commuter rail (or Northeast Corridor) in general. It is an issue on long distance rail as I understand it especially when passenger trains get off schedule which is often.
Having ridden the Northeast Corridor end-to-end the entire route, by far the worst section to traverse on Amtrak is western Connecticut. Which also happens to be the only bit of the NEC that Amtrak doesn't own--it's owned by Metro North instead.