Bugs that should be fixed in a further update.

[Googolplex]

You can always upload your modification to the game as a "Game Enhancer" sorta mod that people can download. As for the last control room puzzle, I never actually encountered that bug myself. Perhaps it's only triggered if you touch around the levers after completing it, but by making it == 4, then you're required to execute the bug in order to finish the objective. Perhaps you should adjust that? You could always try actually patching the bug instead of working around it :3

I'm not a programmer. But you have right, when the total puzzle count is set to 4, then you need to operate all the levers again. But this is better than to have the possibility to skip one of these great puzzles.