Yes!  Always take off the magnets before cleaning your PlanetBox.  Try storing the magnets on the refrigerator until your PlanetBox is clean and completely dry.  And no worries, the magnets are optional so use them only when you wish.
If you do choose to use the magnets, they are designed to be used on the top of your PlanetBox lid.   Please do not put them on the inside of the lid, next to your food.   The magnets are not designed to get wet or to come in contact with foods.