Batman is a man who has his own strong moral code, which can often cause him to clash with his friends, family, and fellow heroes. He is a man striving to do right, but it's always his version of what's right. And sometimes, that can lead to bad decisions with terrible consequences for himself and the entire DC Universe.
Batman would still have to work with teammates and friends who had been disloyal to him, making him chose to either forgive them and move on, or carry it with him, brooding on it. Regardless, the betrayals Batman encountered throughout his history have defined his character and shaped the kind of superhero he is today.
Zatanna And Others Erase Batman’s Memory
In Identity Crisis, after catching Doctor Light for the beating and assault of Sue Dibny, Zatanna and some of the Justice League decide to neuter Light's mind and make him docile. When Batman objects, Zatanna wipes his memory of the incident, altering his mind in a shocking breach of the team's moral code.
Zatanna is a master magician, so her ability to do this is not in question. It is the ethics of the situation and one leaguer basically altering the mind of another that is a devasting break in trust. When Batman discovers the truth, his anger at the disloyalty leads to him creating Brother Eye, which leads to further heartbreak and betrayal.
The Creation Of Brother Eye
After finding out Zatanna and the JLA had erased his memories, Batman is deeply hurt and unable to trust his friends. Bruce believes they cannot be trusted. He builds and launches "Brother Eye," a satellite designed to spy on and gather information about every metahuman on earth, to keep tabs on them so he knows what they are doing at all times, to spy on them.
In Countdown to Infinite Crisis, the system is hacked and used to hunt and kill metahumans. Bruce is now not only spying on his friends but is at least partly responsible for getting them killed. This is not the first nor last time Bruce's paranoia got the better of him and caused disaster for himself or others.
Two-Face Returns to Crime
Batman has long tried to rehabilitate Two-Face, and cure him of his villainous ways. He has always felt responsible for Harvey's mental breakdown and hoped to get him back for his old self, somehow. In Batman: Face the Face, Bruce thought this time he had succeeded and had brought Harvey back from the darkness.
Two-Face was too strong, too deep within Harvey not to come out again. When Dent transformed back to Two-Face, he goes on a killing spree leaving four officers dead and Batman having to hunt him down. Batman blames himself for the deaths of the officers, and for Two-Faces return. Harvey is not as strong as Bruce had hoped, not able to channel the pain and turn away from the darkness, no matter the resources that Batman offered him. He chose Two-Face over Batman.
Superman Hunts Bruce And The Metahumans
Superman's motives might have been good, but his betrayal of Bruce and other heroes in Miller's The Dark Knight Returns can't be overlooked. Superman took the side of the government against his own friends, enforcing the order that forced them either underground or into retirement.
When Bruce as Batman resurfaces, the government calls on Superman to shut him down. Once more, the Man of Steel puts the government over those he called his friends and hunts them down to destruction. It is a betrayal of his fundamental mission, to protect the underdog and do no harm. It is against everything that Superman once saw as important.
Jason Todd Rejects Batman
Jason Todd was the second Robin, supposedly killed by the Joker. Or was he? Turns out Jason didn't die, but had been found and spirited out of the warehouse just before it exploded. He was revived, but his personality has changed; he has become angrier, more brutal, and ready to turn against his mentor.
In Batman: Under the Red Hood Jason adopts the Red Hood persona, blaming Batman for not saving him. He also blames Batman for teaching him a worldview about justice that Jason believes to be a lie. The only justice Jason believes works is one that usually leaves criminals paralyzed or dead after their unfortunate encounters with him. The former Robin feels betrayed by his onetime mentor because the Dark Knight's high moral code didn't prevent him from being killed or letting the Joker continue his reign of terror.
Damian Wayne Joins Superman's Authoritarian Regime
Damian Wayne was trained by the head of the League of Assassins, Ra's al Ghul, to think and fight like an assassin. As Batman's sidekick, Damien clashes with his father's strict moral code of fighting crime to never kill anyone regardless of what they have done. As a result, Damien is resentful and feels that his father is holding him and himself back on their war on criminals.
In Injustice: Gods Among Us, as Superman starts his authoritarian world take over and Batman attempts to stop him, Damian sides with Superman against his father. Damian rejects his father's morality and embraces that of his enemy. Batman will now have to fight against his own son who has rejected the moral code he based his life on.
Batman Helps Defeat the JLA
Batman is a planner, driven by logic and wary of anyone who has too much power. It is only logical for him to have a contingency plan in case the JLA goes rogue and misuses its power. He sees no problem in figuring out how to defeat every member of his team to protect humanity.
In JLA #43–46, Ra's al Ghul, knowing all of Batman's secrets including his identity, finds those plans and uses them against the JLA. The trust the League had in Batman is been shattered. In making those plans, and in allowing them to be hacked, Bruce has broken the sacred bond of trust and friendship with each member. It would be a while before the rest of the Justice League trusted Batman again.
Thomas Elliot Turns On Bruce Wayne
In Hush, Thomas Elliot is a selfish and greedy man. As such, he resents his rich parents and the way he feels they treat him. To get his parent's money, he tries to kill them by cutting the brakes on their car. When Thomas Wayne saves his mother's life, that hate is now focused on the Waynes, especially his former friend, Bruce.
Elliot pretends to be Bruce's friend, all the while acting against him, and trying to destroy him, Wayne Enterprises, and Batman. His hatred for Wayne has consumed him to the point that he teams with a killer like the Riddler to achieve his goal of bringing down Bruce.
Jason Todd's Mom Sells Him Out To The Joker
In the seminal comic book story A Death in the Family, the Joker kills Jason Todd in his Robin identity. Jason had never met his mother believing her to be dead. When he finds her alive as an aid worker in the Middle East, he is ecstatic. Jason is desperate for a parental figure, and while Dick Grayson has become something a big brother, Bruce can still be distant and cold.
After losing his father and stepmother, Jason put too much trust in an ill-formed motherly bond that turned out not to exist at all. His mother sold him out to the Joker and Jason's desire for a parent led to his brutal beating and supposed death in a warehouse bombing.