I found out the problem and the solution!
So what was happening is that certain objects were not getting destroyed and it was messing up the entire game.
Solution: Make families that destroy everything when they move scenes. So you have to make a family for game objects, a family for text objects, a family for particles, basically a family for any kind of game object and when you move scenes you have set all families to destroy.
For future, perhaps we can add this automatically to the change layout. This would cause future distress. Or perhaps a system-destroy all feature.
This would be very usefull for bigger games. My game isn't the biggest and it was still causing problems