When she feels an urge, the puppy will usually let you know by whining and scratching. That’s her signal that she has to go and wants out of her little den. Now! Don’t delay because if you let your pup lose control in her crate, she’ll get the idea that it’s OK to mess up her living space. Then she’ll think nothing of leaving little packages around where you live, too.

Just so you know, a puppy is never completely housetrained until they are 6 months old. For some breeds, even later. This means that though you may be making tremendous progress housetraining, there will be "mistakes". Sometimes for reasons you can't figure out! Don't fret about it. Stay focused on the progress you are making. Your confidence in the techniques you are using to house train your puppy will ensure your success.
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.
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.
One of the easiest ways to prevent accidents is learning to recognize when your puppy needs to go out. Most puppies will sniff the ground when they’re getting ready to potty, but there are many other more signals that happen prior to sniffing. Puppies that pace, seem distracted and walk away from play are subtly signaling that they have to go out. If your puppy tries to sneak out of the room, take a potty break right away.
Just because your new dog is old enough that he should know where to potty doesn’t mean that he actually does. An adult dog has the necessary muscle control to hold it for longer periods of time, but if no one ever taught him the potty training rules then he’s the equivalent of a brand new puppy. Age should not be equated with housetraining prowess, so it’s a good idea to treat any dog new to your home as if he’s still learning the potty training ropes.
According to a January 2007 article in the Indian scientific journal Current Science, some professional dog trainers find Millan's methods outdated, flawed and "unscientific and inhumane."[35] Millan's detractors say that what Millan calls "calm submission" is actually a state of helplessness that is the result of averse dog-training techniques.[35] A study in Applied Animal Behaviour Science said Millan has been influential in popularizing punitive techniques, but that bad behavior from dogs was caused by fear and anxiety, not a lack of the owner's alpha status.[36] Malcolm Gladwell, writing for The New Yorker, said that critics were responding to a "highly edited" version of his approach on television, which exaggerates the frequency and intensity that he uses when he disciplines the dogs.[35][37]
There is nothing inherently wrong with telling your dog “no,” except that it doesn’t give him enough information. Instead of telling your dog “no,” tell him what you want him to do. Dogs don’t generalize well, so if your dog jumps up on someone to say hello and you say no, he may jump higher or he may jump to the left side instead of the right. A better alternative would be to ask him to “sit.” Tell him what you want him to do in order to avoid confusion.
If your dog exhibits a behavior you don’t like, there is a strong likelihood that it’s something that has been reinforced before. A great example is when your dog brings you a toy and barks to entice you to throw it. You throw the toy. Your dog has just learned that barking gets you to do what he wants. You say “no,” and he barks even more. Heaven forbid you give in and throw the toy now! Why? Because you will have taught him persistence pays off. Before you know it you’ll have a dog that barks and barks every time he wants something. The solution? Ignore his barking or ask him to do something for you (like “sit”) before you throw his toy.
Suppose you consistently praise your puppy for their actions, while potty training. Then say your dog has an accident. Do not praise you dog immediately. Instead, take your dog outside and wait for it to go to the bathroom. When it finishes doing its business, take it inside, and keep it in a separate room while you clean up the mess. After this you should act disappointed in your dog, but only for a few minutes. Keep you and your dog motivated to potty train.
In 1935, the American Kennel Club began obedience trials, and in the following years popular magazines raised public awareness of the benefits of having a trained pet dog, and of the recreational possibilities of dog training as a hobby.[19] After WWII, the increasing complexities of suburban living demanded that for a pet dog's own protection and its owner's convenience, the dog should be obedient. William Koehler had served as principal trainer at the War Dog Training Center, in California, and after the war became chief trainer for the Orange Empire Dog Club—at the time, the largest dog club in the United States—instructor for a number of breed clubs, and a dog trainer for the Walt Disney Studios.[20] In 1962 Koehler published The Koehler Method of Dog Training, in which he is highly critical of what he calls "tid-bit training techniques" based in "the prattle of 'dog psychologists'".[19] Amongst the training innovations attributed to Koehler is the use of a long line in conjunction with a complete absence of oral communication as a way of instilling attentiveness prior to any leash training. Koehler insisted that participants in his training classes used "emphatic corrections", including leash jerks and throw chains, explaining that tentative, nagging corrections were cruel in that they caused emotional disturbance to the dog.[21] Vicki Hearne, a disciple of Koehler's, commented on the widespread criticism of his corrections, with the explanation that it was the emotionally loaded language used in the book that led to a number of court cases, and to the book being banned in Arizona for a time.[22] Despite the controversy, his basic method forms the core of many contemporary training systems.[23]

Once he seemingly has this idea down, move the string of bells to the left or the right of your dog and see if he moves to go and hit them with his nose; if he does click and treat! Next try moving the bells above his head and then closer to the floor. If he is chasing them with his nose in an attempt to ring them, then he understands what you want!
While working with a dog, Millan often uses vocal marks such as tsch,[33] gestures, and body language to communicate with dogs rather than speech or the dog's name. Millan encourages owners to create their own unique sound that works for them.[32] He believes that dogs sense, understand, and respond to a person's energy more easily than their speech.[34]
There is nothing inherently wrong with telling your dog “no,” except that it doesn’t give him enough information. Instead of telling your dog “no,” tell him what you want him to do. Dogs don’t generalize well, so if your dog jumps up on someone to say hello and you say no, he may jump higher or he may jump to the left side instead of the right. A better alternative would be to ask him to “sit.” Tell him what you want him to do in order to avoid confusion.
Marian Breland Bailey played a major role in developing empirically validated and humane animal training methods and in promoting their widespread implementation.[14] Marian was a graduate student under B.F. Skinner. Her first husband Keller Breland also came to study with Skinner and they collaborated with him, training pigeons to guide bombs. The Brelands saw the commercial possibilities of operant training, founding Animal Behavior Enterprises (ABE). In 1955, they opened the "I.Q. Zoo" as both a training facility and a showcase of trained animals. They were among the first to use trained animals in television commercials, and the first to train dolphins and whales as entertainment, as well as for the navy.[14] Keller died in 1965, and in 1976 Marian married Bob Bailey, who had been director of marine mammal training for the navy. They pioneered the use of the clicker as a conditioned reinforcer for training animals at a distance.[13] ABE went on to train thousands of animals of more than 140 species.[14] Their work had significant public exposure through press coverage of ABE-trained animals, bringing the principles of behavior analysis and operant conditioning to a wide audience.[15]