The only time I use ONE SHOT is to photograph buildings, bridges, and distant scenery. AI-SERVO keeps the focus lock on the moving subject. No exceptions! Although ONE SHOT may make sense, during the fraction of a second between focus lock and shutter open in ONE SHOT, the train moved, and will be slightly blurred as a result. That one 'got me' a couple months ago.Р”Р„lso, rule one for all Canon cameras.if it moves, use AI-SERVO. It's also possible that you've inadvertently moved the AF switch to MF. Perhaps that's in the wrong position for your shooting. If memory serves me, the Canon 100-400 also has a multiple Image Stablization setting switch. Also set the 'lens drive when AF impossible' to OFF, otherwise your lens and camera will 'go nuts' trying to focus when it cannot do so, such as quite low lighting. I rarely miss focus as a result.Р”Р„lso, if your camera has such AF settings, ensure you have set the AI Servo image priorities to either the middle or 'focus' settings. For what it's worth, I've set my camera to use only the center focus point. The AF will most often choose the closest item to focus on, perhaps a tree leaf 20 feet away, or a nearby building rather than on the train that's 100 yards away.

That's one of the major problems when shooting in Auto mode. I'm guessing you are letting the camera choose from any of its maximum 9 or 23 or 61 AF points rather than 'locking it down' to just a few possible focus points.

Canon micro focus adjustment