I think that's an original game bug; The controls will be fixed in a few, that's my end.
Maybe it's an original bug, but to be sure, I played the Arcade version sometimes in the 80's and I can't remember something like that. But everything's possible, maybe I was just lucky, never to encounter this bug back then?
Last short question. Have you ever compared the game-speed, at which your Phoenix version runs on an Amiga500, compared to an A1200? Has the player full speed on ECS/OCS Amigas too? It almost looks that way in emulators, when i compared, but I'm not entirely sure (and I don't have a real A1200 Amiga).
By the way, I don't mean to digress, but since we're on the topic of the very nice game-classic "Phoenix". You know what would be really great too? If someone ported the Atari VCS-2600 version of Phoenix to the Amiga or the C64. While the Atari-2600 version is quite different from the Arcade original, it's also fantastic as a game in its own right and plays really well. This version in an exact 1-to-1 port, would also be absolutely amazing on the Amiga or the C64. You make nice Amiga ports of Arcade games, maybe someday you also want to port a Atari-2600 game to the Amiga, then this game would be superb. :-)