So in a lot of games their are some that have a New Game and New Game + Category. I ran into a problem with a game I ran and noticed that after the game is beaten, you are able to skip a puzzle you do the next time you play, and the only categories for the game are Any% and 100%. Do you think the puzzle is or isn't required for Any%? The run submitted did the puzzle and other submissions are being sent in with the puzzle being skipped. Which is the correct action?

What game is it? And NG usually means that you start from a fresh save, so if you do that and are able to skip the puzzle, then yes it should be skipped. However, if it is loading a file into a new game, then it is NG+