This is an excellent puzzle game, and the mechanic of the game fits perfectly.
the bugs can break entire levels. I think you tried to use physics instead of making a grid-based game, and in this types of game, it generates all those bugs. Instead of using the physics engine of unity to push diferent things, you should use transforms and animations. that way, the player, the cristal and the box will always be at the center of the grid square and the physics engine wont do weird things like pushing the crystal to the side (but this requires much more coding than using the physics engine, so its understandable if you dont want to change it).
you could also maybe fix the issue by making the box collider of the box a little smaller than the grid square, and if you are using a capsule collider for the crystal, changing it for a box collider (to avoid pushing the crystal to the sides when it should move forward). this would be a lot easier in comparison to having to write entire new code for the game mechanics
Overall, the game is really fun, and the puzzles are great, Good job :D