The Doctor is a complex character. He regularly regenerates to become a new, slightly different version of his (or, recently, her) past self. With each regeneration comes more complexity; the creators have to keep the character new and interesting while negotiating new characteristics with old ones.
This proves tricky, as we can see through the many inconsistencies in The Doctor's behavior. It begs the question, how much are we supposed to believe The Doctor holds onto with each regeneration and is it possible that he is just a bit flaky? Here are ten times that The Doctor went against his own values.
Taking Amy On As Companion
Leading up to Matt Smith's first episode, "The Eleventh Hour", The Doctor has once again faced heartbreak at losing companions who were very dear to him. As a result, he has vowed to no longer enlist any further companions.
He said a similar thing before taking on companion Donna Noble, and that ended badly--with Donna having to have her memory swiped, forgetting all of her relationship with him. Next thing we know, in swoops the next Doctor, seemingly suffering some kind of amnesia or simply choosing to ignore the previous Doctor's promise to take on no further companions in fear of putting them in danger, as he quickly gets himself a new one--Amy Pond.
Every Time He Meets a Past Self
The Doctor, in various regenerations of himself, has frequently asserted that it is in the best interest of the universe that he does not interact with versions of himself from other time streams.
He also repeatedly breaks this rule, occasionally throwing in some half-baked explanation as to why its OK to do it this time--but there are many occasions when he gives no explanation at all, leaving us to think--okay, according to you, all of time and space should be exploding at any moment now...
Promising To Keep People Safe
He's guilty of it again and again. With every new companion and countless civilians he meets across galaxies, The Doctor makes the promise that he won't let anything bad happen to them.
But while he does pretty much always save whatever planet he's on, he does not always come through in saving every person he meets on that planet. This usually ends in tears and awkward, deeply surprised apologies on The Doctor's part. It seems that in the thousands of years he has lived, he has not learned to just stop making promises that he can't keep.
Using A Gun
Every iteration of The Doctor is anti-gun. This quality is particularly strong in the David Tennant version of The Doctor, who adamantly refuses to use a gun even when it might save himself, or an entire planet. It's shocking, then, when in the "A Town Called Mercy" episode of Matt Smith's Doctor, he willingly wields a gun as appointed mayor of the town.
Now, to choose to break his sacred rule in order to save a town, when in the past he wouldn't do it to save the earth? This is quite uncharacteristic of him.
Trusting The Master
Peter Capaldi's Doctor proves himself to be the softie The Doctor often reveals himself to be--to the point of naïvety, in this case. Through much of season 9, The Doctor is made out to be protecting and/or guarding a mysterious box, contents unknown.
That is until it's revealed that what he is guarding is a woman, an apparently dangerous woman with a dark past whom he believes he can get to see the light. Surprise surprise, it's a future regeneration of the hateful Master. The Master has proven himself, again and again, to be cruel-hearted, and even carries out a ten-year plan in which he tortures and then converts The Doctor's loved companion, Bill, into a cyberman...after which The Doctor pleads for him to join forces with him, still.
Leaving Amy Behind
Matt Smith's Doctor takes Amy and Rory on a trip and they end up on a planet faced with two doors to choose from. Amy chooses one, and The Doctor and Rory mindlessly choose the other.
Long story short, Amy is put on a sped-up time stream where she ends up living on the planet for 50 years in the time they are their maybe an hour. By the end of the episode, The Doctor opts to save the young Amy and leave the old Amy behind to die. This does not exactly fit with his vow to always protect Amy...arguably, he leads her to her death.
Letting River Song Fly The Tardis
The Doctor never explains how the Tardis works to anyone. As far as we know, The Doctor and his Tardis are a package deal, two intricately connected entities shrouded in mystery--and that's part of the charm. Then comes River Song, and the charming mystery is thrown out the window. For what? The sake of once again trying to make River Song look cool and special, an opportunity for her to land a smug one-liner?
River Song as a character defies many of the established foundations of The Doctor, and it serves to disrupt some of the appeal of the show. The last straw is when she claims that the only reason that the Tardis makes its signature noise is because The Doctor leaves the breaks on...this is borderline blasphemy.
Inviting People To Witness His Death
Matt Smith's Doctor sends Amy, Rory, and River Song mysterious letters inviting them to a particular place and time. This turns out to be The Doctor inviting them all to witness his death during a casual picnic in the desert. It's later revealed that his reason for doing this is because he didn't want to die alone.
This goes against his staple principle of avoiding putting people in danger. By inviting them, he makes them witness to an event where River Song exists in two temporalities at the same time--something he has claimed can tear the universe apart. Yet, as usual, he puts not wanting to be alone over the safety of others.
Exploring With Bill
Similar to his past vows to no longer take on new companions for fear of them meeting certain doom, with Peter Capaldi's Doctor in season 9 we find him working as a solitary professor, keeping a low profile and avoiding travel.
In comes Bill, chipmaker with the potential for more--a typical archetype for the Doctor's companions--and just like that, the Doctor is traveling again and putting someone else in danger. Spoiler, Bill does meet a horrible doom--and the Doctor takes on more companions after her.
Leaving Oswin Behind
Oswin, or the earliest version of Clara that we see, is found in the form of a human-turned-Dalek. The Doctor has only interacted with her voice when he promises to save her from the ship she is stuck in--and then he realizes that she is in fact a Dalek who used to be a human, and who was so traumatized by being turned into a Dalek that her mind convinced itself she was a human stuck in a ship.
Now, The Doctor prides himself in being the protector of humankind. Yet, he treats Owsin with disgust and leaves her behind.