Hence, the acceleration and braking systems were optimized for automatic operation (as opposed to manual operation) and it is difficult for a human driver to control the train's movements precisely and smoothly.
I have a perspective on this that most probably don't, as I was a monorail driver at Disney World for a number of years. Contrary to what some might imagine, the current Bombardier Mark VI trains there are not attractions but are in fact full-up transit vehicles, and Bombardier continues to sell them as such (although with different bodies and newer electronics). If D.C.'s trains handle anything like ours did, I can understand why some of the drivers short-stop or otherwise have problems.
Our Mark VI trains were originally designed to accommodate automation as well, but I don't think this in itself really is a factor. More importantly, each train had its own "personality" and handled differently, and all of them would take between one and two seconds to respond after an input was commanded except for E-stops, which instantly opened the relay contactors and applied air to the friction brakes. One train might be ultra-responsive (relatively) to the throttle and have really tight brakes, which made it easy to drive and predict stopping distances with great accuracy. Others would act like your control inputs were more of a suggestion than a command, necessitating that you be looking a little ahead of where you actually wanted to be in order to stop where you were supposed to. We had some drivers that had difficulty dealing with that, and would often blow their stops by a couple of feet or so on a train with loose brakes, or would stop short if they were in a tighter train that didn't require so much anticipation of its behavior. I don't think I ever had a short stop, but did have trains "slide" on me a few times and missed the stop by just enough to have to back up a couple of inches to get lined up with the gates.
I would imagine transit trains everywhere exhibit similar unique peculiarities, and the only consistent way to deal with it is for the driver to be ultra-conservative, which can lead to the occasional short stop. It's not so much a problem for an automation system that can directly respond in milliseconds and isn't being moved between trains with wildly varying performance characteristics.