This same thing has happened to me on the XBox at least 4 or 5 times. Each time I have been in map view, had an active maneuver node on the orbit path, been attempting to change direction and when I release A, a new window pops up for something that was underneath the active handle. When I close that box I am no longer able to use any of the A buttons functions.
My first experience with this game has been on the console this week. I absolutely LOVE it. Enough to constantly quit and reload the game, which is the only solution I have found.
It is possible to quicksave after the bug occures and resume from there with full functionality after a game restart.
Being new to this game, it is possible I'm entering a view/mode change that I am unaware of, but I have not been able to determine what has changed.