This happens all the time and it's so freaking annoying. I just lost a game in part because of it. I tried to save the video but for some reason my PS4 only saved a 4 second clip.
But here's what happened: 0-0 in the 85th minute. My opponent sends a through ball to Lukaku that goes too long, so I have Manolas controlled by the AI running to get the ball; I had been using De Rossi. I press the switch button to take control of Manolas and retrieve the ball. A split second before I press the button, however, I'm auto-switched to Manolas. When my pressing the switch button registers the game then switches me off Manolas and to Criscito who is off the play. Manolas, of course, stops in his tracks because he's now under AI control again and evidently decides there's no reason to keep running after the ball. By the time I switch back to Manolas, my opponent is in clean with Lukaku for the winner in a 1-0 match.
Manual switching is really "sometimes" manual, when the game doesn't decide to auto switch you anyway. I find it so annoying.