It’s always been fairly common for the Northern stoppers between Leeds and York or Selby/Hull to be held if there’s a TPE or XC running a few minutes late which should be going ahead of the Northern train. Northern tend to use one of the southbound bays at York while TPE and XC use the through platforms furthest from the main entrance, so I can see it causing problems if a slightly delayed train picks up more delay from following the stopper and then has to be pathed across the southern end of York station, potentially delaying southbound trains as it goes.