When you decide to have a pet that is meant to be a wild animal, such as a rabbit, then you are going to have to deal with some natural behaviour of the rabbit. For example, in the wild, rabbits dig to create burrows for themselves. Not only is digging a natural behaviour, but rabbits also seem to really enjoy digging. Your pet rabbit should never be punished for digging. This will not fix the problem and could cause other behavioural issues. If you want to stop your rabbit from digging burrows, you need to redirect the behaviour and use simple training techniques.
Correct your rabbit when it starts to dig where it is not allowed. Clap your hands loudly and follow with a simple "No" command. Then, remove your rabbit from the area.
Cover the area where your rabbit loves to dig burrows the most to restrict it. Until you feel your rabbit is better trained, do not allow access to this area.
Give your rabbits areas where digging is allowed. Again, digging burrows is a natural behaviour that your rabbit should not be denied altogether. A digging box or grass mat are areas where your rabbit will enjoy digging.
Supply your rabbit with a lot of toys. Make sure the toys are safe for rabbits. Keeping your rabbit amused will help deter digging behaviours.
Find a balance between letting your rabbit roam and keeping it in a cage. A rabbit should not be confined to a cage all day. Reserve the cage for a few quiet hours per day. If you keep your rabbit locked in a cage too long, it will become bored, frustrated, aggressive and even destructive. Behaviours such as digging will become more of a problem. A well exercised, happy rabbit is a better-behaved one. On the other hand, a rabbit that never spends any time in a cage will likely adopt more destructive behavioural patterns.
Make sure your rabbit's cage is big enough. It should be a pen that's large enough for your rabbit to move around freely and get exercise within the cage. The cage should be equipped with fresh hay and rabbit-approved toys.