Hello Azecy, Thanks for the Feed back.
I knew it was inevitable that I was going to have people run into bugs/glitches despite playtesting and having my friends test it. My friend had a similar issue with the final boss and I could not figure out why the bug occurred. I think you are right and that may be the source of the bug.
I'm not sure about the checkpoint box freezing the game. I know the game is supposed to freeze for a few seconds before the click button to continue pops up. If you have any thoughts to why that happened I love to hear them for future projects.