The two main reasons for dog digging are that your dog may be too hot or too cold.
When your dog digs a hole and lies in it, his temperature can be self-regulated.
Unlike humans, dogs can't remove their clothing or add layers, so they have to come up with other ways to get relief from the weather conditions.
Dogs also dig because they are bored.
Dogs can become very bored and restless when their owner is away for an extended period of time.
A dog that is left alone will find ways to entertain himself.
Sadly, this might be digging! To stop dogs from digging, their behavior needs to be redirected towards other activities.
Sometimes all you need to do is provide him with a safe digging area where there will be no repercussions.
Certain dog breeds are inherently prone to digging.
It will require additional patience to stop certain breeds from digging.
The following tips should help to stop dogs from digging up your yard:

1. Put an unpleasant "present" in the hole dug by your dog.
   Often dogs dig for a while, then leave the hole for a period of time, and return later to continue their digging activity.
   Once your dog has left the hole, you should place the "surprise" in the hole.
   One suggestion is water sprayed with bitter apple, which is available in pet stores.
   
2. Another way to discourage your dog from digging is by putting garden waste in the holes.
   Dogs prefer to dig in "clean" dirt.
   You should put mulch, sticks, dead vegetation, and rocks in the hole and lightly cover it with soil.
   When your dog resumes his digging and discovers these undesirables in his hole, it is likely that he will stop digging.
   If you find that this doesn't work, try filling the hole and spraying it with bitter apple.
   Most dogs will cease to dig in that spot as they dislike the smell.
   
3. Give your dog his own spot where he is free to dig without fear of punishment.
   Digging is natural for dogs.
   Training your dog to dig just in that spot may take time but it is possible.
   One way to stop dogs from digging up your flowers is to provide them with an area in the garden where they can dig as much as they like.
   You could use a sandbox or fence off a portion of your garden that has not been landscaped.
   In order to teach your dog that he can dig in a particular spot, you should bury some treats where he can easily find them.
   If you have previously scolded him for digging, you may need to give him extra encouragement.
   He will be a delighted pooch as soon as he discovers that he is permitted to dig in that spot.
   
4. When your dog has been provided with his own designated spot for digging, you will still need to keep things interesting for him.
   Once in a while, a toy or snack should be buried as a surprise for him.
   Dogs get bored with digging the same patch of land and may find another spot in your garden more exciting.
   Periodically, the dirt or sand in your dog's designated digging spot should be replaced.
   Dogs prefer fresh dirt to hard earth.
   There will also be times when your dog will prefer your flowerbed to his own digging area.
   Spray your flower borders with animal essence, which hunters use to tempt animals.
   The odor from other animals may discourage your dog's digging.
   

These tips will help to stop dogs from digging in areas other than the designated spots you have assigned to them.
Dogs are not being mean when they dig under your fence as this is instinctive behavior for them.