If you know that there is a glitched Pokemon in box 6 that is causing your game to crash, then I would recommend using a code to replace the glitched Pokemon with a valid one.
In PokeGen, fill out the details to make a Pokemon. Then click the drop-down list and select "Box 6". Right-click on each slot, and press "Set" to fill Box 6 with the Pokemon that you created. By left-clicking on the Pokemon to toggle them, make sure that only the Pokemon in the first row are selected and highlighted in blue. Then press Tools -> Code Generator. Select your game from the drop-down list, and then checkmark the box that says "Selected Pokémon (6)". Now press the Generate button to get a code that will overwrite the first row in Box 6 of your game. Press the Select button to activate the code in your game, and check if Box 6 is fixed.
Repeat this procedure to make separate codes for the other rows in Box 6. But make sure that you only run 1 code at a time.