Young puppies can’t hold their bowels & bladders for long. If you come home to find that they’ve had an accident in there it’s quite possible that they can’t hold it that long. Generally puppies can hold their bladder for about one hour per month of age. So your 3 month old pup can probably only hold their bladder for about 3 hours. If you’re going to be away at work for long periods of time see if you can get a neighbor, relative or dog sitter to come over to let your pup out during the day.
If your dog isn’t giving you an obvious signal that they need to go out (like whining at the door) I suggest teaching them to ring a bell when they need to go outside. Some of the other signs dogs give that they need to go out such as pacing around or circling can be easy to miss if they’re in another room, which is why a noise based signal such as ringing a bell can make things easier.
Confine your puppy to his, 'puppy-proofed' bathroom or an exercise pen and paper (or wee-wee pad) the entire floor. Put his bed, toys and food/water bowls there. At first there will be no rhyme or reason to where your pup eliminates. He will go every where and any where. He will also probably play with the papers, chew on them, and drag them around his little den. Most puppies do this and you just have to live with it. Don't get upset; just accept it as life with a young puppy. The important thing is that when you get home, clean up the mess and lay down fresh papers.
Remember that training is an ongoing process. You will never be completely finished. It is important to keep working on obedience training throughout the life of your dog. People who learn a language at a young age but stop speaking that language may forget much of it as they grow older. The same goes for your dog: use it or lose it. Running through even the most basic tricks and commands will help them stay fresh in your dog's mind. Plus, it's a great way to spend time with your dog.
Unless you plan to keep your dog outdoors--and few of us do because it's not recommended--you'll need to teach your dog where to eliminate. Therefore, house training (also called housebreaking or potty training) is one of the first things you need to work on with your dog. Crate training can be a very helpful part of the training process. This includes house training as well as many other areas of training: