Please forgive the length but I am offering a complete detailed article on what happened in that three part series.
I, too, was appalled at how Dr. Phil manipulated his show to paint this young father guilty of child molestatioin and to make the young woman appear straight as an arrow. As a former police trainer, actress, and 20 year journalist, let me share with you what I saw. By the way, it may shock some viewers of that three part series even further to know that "Dr." Phil McGraw made a very brief, butt saving, underwhelming announcement after the show's credits ran -- thereby eliminating many of the viewers -- that the young man had taken two polygraph tests paid for by the show budget, not one. And that further, he had passed one of the polygraph tests. Some late watchers taped this very brief backpedaling by McGraw.
Here is how McGraw set up the young father imho:
He placed him in an adversial position, head on with him, and screamed at the man, bullied him, and aggressively negated any defense the seemingly slow thinking young man tried to make. He baited the yojng man mercilessly.
In contrast, McGraw positioned the young woman sitting next to him on a small sofa, very cozy with him --  and even when he --gently -- suggested she may have coached the little girl t make this accusation, he soft pedaled all he said. He was clearing the decks for her in the only way he could -- pooh poohing this act away as "nothing serious." Which he did again when she failed the part of the "Poly graph" (more sensationalism for the ratings-- another "cliff hanger") -- that she had already admitted to doing. Clever, clever McGraw.
Coaching a child to say her father touched "my pee pee", is very very serious in a court case. I have seen one mother lose custody of her five year old daughter for doing that.
McGraw repeatedly showed the film the mother had provided of this three year old crying and saying "He touched my pee pee." Never did the child say "My daddy touched my pee pee." Isn't that a bit strange?  Why
didn't this very intelligent professional questioner pick up on that? No controversy, no show, folks.
Further, McGraw screamed at the audience that polygraphs are 92 percent accurate. We all know that is not true. They are not allowed in court because their rate of INACCURACY is so high they are not considered dependable.
Next, McGraw badgered the young man's new wife, literally bullying her into changing her statement of total support for her husband to "I don't know. He failed the lie detector test so now I don't know what to think."
He even bullied her into saying to the mother, who had a free ride if I ever saw one, that she would not want to endanger the child --as if she did cooperate in that act! McGraw literally put the words into the young pregnant woman's mouth and bullied her into saying them.When her husband tried to defend her, McGraw opened up the box of slurs he had in waiting. He growled that the young woman had an affair and the child was not the young man's! Since the man seemed to be totally aware of this fact and not disturbed by it, why would McGraw air it? Just to discredit the woman. Nothing more. Totally unscrupulous. He may be a showman, as has been said, BUT HE REPRESENTS HIMSELF AS A PROTECTOR OF CHILDREN AND A PROFESSIONAL THERAPIST. HELLO? Why would a protector of children air this awful tape of this helpless child. And then say over and over, "I am all about Kaylee" mentioning even her name on air. Hey, we as journalists have a code NOT to out an underage child. No matter what mom and dad say.
Worse, McGraw represented his polygraph tests as "completely objective." Hogwash. Even that part of his show was designed to condemn the young father.
The so called polygraph expert (allegedly in  the narrow field of child molestation( said on air that the father tried to manipulate the exam to win. (After McGrw led the quesiton) That the young man had obviously used the internet to find out how to beat the test. Well, your own site tells how.. . and each thing listed on the Internet was used by THE MOTHER!
Mommy sat as calm and relaxed as if she was meditating with the Dalai Llama.   Coached and reassured of the results prior to the test????
On the other hand, the father was very emotional and once weeping  while obviously answering the examiner's questions. Mother said nothing -- not a peep_ but "yes' and "no."
Father's replies were emotional and not just "yes" or "no". Here's the clue: the audience NEVER HEARD THE EXAMINER'S QUESTIONS. The man was set up to look out of control.
This is the most unethical television program I've ever seen.
If I sound passionate, it's because of what happened to my neighbor and her son recently.

My neighbor, who is in her 60s, works at Wal-Mart. Her middle aged son, who lost his good job in Dallas when the downsizing, outsourcing hit Texas in full force, moved in with her until he could pull his life together again. He had lost his income and his apartment. Her income and her late husband’s social security payments kept them afloat. Then he found a decent job. They started to pull out of their poverty spiral. Let’s call him John, although that's not his name.
The elderly mother was at work that night at Wal-Mart. Her son was at home alone. A knock came at the door. He opened it part way. Before he could identify the two men at the door, they pushed into the apartment and attacked him with a baseball bat. As they hit him in the head with the bat, one shouted, “If you ever talk to MY kid, I’ll come back and kill you.” Then they walked out, leaving John seriously injured on the floor.  
Now John is unable to work; his memory is severely limited. His neurologist says the assault damaged his brain. Today, he lost his job. NOW GET THIS. THEY HAD THE WRONG ADDRESS. THEY HAD THE WRONG MAN. THEY EVEN HAD THE WRONG AGE MAN! It seems a younger man of 20, who had been arrested at age 12 for molesting a 2 year old, lived somewhere near by. The police have not caught John’s assailants BUT HE WILL LIVE WITH THE RESULTS OF THEIR ASSAULT FOR THE REST OF HIS LIFE.
McGraw, when the young man expressed fear that he might be "mugged on my way out of the studio," led the audience to applaud enthusiastically. Unbelievable.
As a former journalist and producer on radio, television and print, I am appalled with McGraw. He rode the tail coats of Dateline's Predator series to raise his ratings and position himself as a protector of children. Not true.  McGraw is all about McGraw and his growing empire. I've stopped watching him. I will boycott any products ever connected with him.  Radiogal