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.
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. 

It’s best not to punish the puppy for making a mistake. Instead, focus on praising appropriate bathroom behavior. If you catch your puppy in the act, interrupt it by saying “No!” in a firm voice or clapping your hands loudly, then take the puppy outside to finish going to the bathroom. Never swat your puppy, yell at it, or try to rub its nose in the mess.

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