In the wild digging in soil is essential for bunnies survival so not only does your bunny have an instinctive urge to dig they are also naturally very good at it. If your bunny can get to the soil in your plant pots then it's likely they are going to want to play there and you shouldn't be surprised when you discover a mess has been caused by the soil being flung about. Not only can this cause damage to your floor. The soil could also contain materials that are contaminated with plant food and pesticides that your bunny may eat so it's important to bunny proof your plants to make the soil off limits.
The first thing you should consider doing is moving your plans out of reach. Place it on a solid shelf or piece of furniture well out of reach as you don't want your bunny to tug on it and for it to topple on them. Remember bunnies are good climbers to check they can't find another way to get to them. If you water your plants from the base, make sure this is out of reach also in case your bunny drinks the water as it can be contaminated with plant food.
Another way to stop digging is to cover the soil with a layer of something. Home store stores sell a range of products used to help prevent moisture evaporation such as decorative stones or shells as these can be used to cover the soil.
If your bunny does seem to love digging in things, then it can be a good idea to give them a safe and acceptable alternative to satisfy this need to burrow and forage. A digging box can be a great way of letting them exercise this type of behavior and will keep your bunny entertained for hours.