Is it not the case that it is shot down only once, but the way the 3 timelines are interwoven means we see the same scene from several different perspectives.
The point about the Spitfire's ammo is exactly one that I made to my wife on leaving the cinema, I also commented on the inaccurate appearence of the warships depicted. However, I think that pulling the whole thing apart and marking it down on technical historical accuracy is obscuring the fact that people don't generally go to the ciname to watch documentaries.
I also understand that the director deliberately avoided any use of CGI.