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.
You may also notice common behavior problems in your dog such as jumping up, barking, or even aggression. The best way to correct any misbehavior is to interrupt it. Shift your dog's attention to something positive. Try running through cues that your dog has mastered followed by rewards. Keep your demeanor cool and confident, and be clear about what you mean.
Consistency is crucial. This may mean taking time off work to be there to take the pup outside every 20-30 minutes when they are awake. Crate training will also help the 'penny drop' as it teaches the pup to hold on until taken outside. Then, be sure to stay with the pup in the yard so you are there to reinforce how clever they are when they do go in the right place.
Introduce your new pup to its new home, family and their role. Just like when you are new to a place or group, your new pet may be bursting with curiosity, excitement, fear or joy. Now is the best time to lay out the foundation for a good and pleasant relationship with your pet. For a puppy to settle in and learn to trust and respect you and everyone at home, it is very important to establish your expectations of your puppy and be consistent with them.