You're right, you only need to remove the duplicates and the die will stop giving you penalty. For example, I have the board as below and the 6 is giving me penalty. I will need to remove one of the 9s in order to stop the penalty. My tutorial is a mess so I hope I have cleared any confusion now. Hope you had fun!
Oh right, that must be it then. Briefly before submission I did noticed something strange with the score or the penalty system, but I couldn't figure out what or why, so at the last minutes I wrote a vague warning on the game's page that there would be bugs. You put so much thought into the game and even helped me find the bug and I really appreciate that!
