If you have time and would want to fix them during the jam to get others to play a working version, I think that should be allowed. The jam FAQ says: "You can fix game breaking bugs in your submission and upload those. If your game is unpleasant or unplayable due to technical issues, we want you to fix those! You just cant add new features or gameplay. or things like that." and your game might fell into this category. At least if you don't have to make a lot of changes.
Of course I cannot speak on behalf of the organizers but this would be how I understand the rules.