I just beat the very last level that I had left, and it won't register my 100%. After beating the last level it takes me to the points assignment screen. But the game is trying to award me 2 points (an expert level) and I only have room for assigning 1 more point. It won't let me progress unless I assign that last point, the only thing I can do is quit the game. Then when I restart the game, it doesn't register that I beat that last level...
FYI I also had the same problem as the other commenter the first time I tried to 100% the game. I re-played normal levels to up my stats for the 3 expert levels I had remaining. Then When I managed to beat an expert level it didn't register as complete due to inability to assign the awarded points to the already maxed stats.
That's why the second time around I was very careful just to beat every level once, and I still had the same issue pop up.
BTW I never would have thought I'd get 6+ hours of gameplay out of a pico8 game. Great job.