Which challenges do you have left? I know the mod doesn't beat challenges if you have over the required number for the goal, like as an example you had 90/100 kills then added this mod it would be 90/1 kills which would mess it up. Usually getting another kill would beat the challenge even with the mod installed, but I can see that messing it up. What I did was just edit the goals so that the Challenges Completed and Collectible ones were all default and other ones were close to my progress I had already made.