So I submitted a run which was Rejected because I “Missed The Smurf Coloring and Baking Minigames” chose Papa Smurfs Portal Instead of Bakey and Artist Smurfs Portal The Sio Saves a Ton of time should it be allowed?

The mini-games are the ones that are available in the mini-games section of the game. Papa smurfs portal isn't a mini-game, and even if it was, you would still have to complete all mini-games once like the rules say