Rad, thanks so much!
I think that when choosing the level select option in the pause menu, the game is not resetting a bunch of variables and so we will need to look at fixing all of that - it is clearly bugging out lots of stored variables when returning to other levels.
The crystals currently don't reappear in a level if you get it and then leave immediately, I wanted to make it so you would need to collect the crystal AND complete the level in order for that progress to save (I even designed a few levels that incorporate additional interesting puzzles just with that in mind) but ran out of time in the jam.
I have recently recognized that the move counter can sometimes count extra moves erroneously - we will definitely be fixing this!
Congrats on getting the high scores! It makes me really proud to know that someone out there cared to challenge themselves because they enjoyed the game so much. I made this game for people like you!