Minor Plot hole: Hancock is sent in jail to be reunited with hundreds of inmates he personally arrested. All those prisoners know that he is invincible. Yet, they still try to threaten him until he cartoonishly shoves an inmate's head up his ass.
Major Plot hole: In a 'shocking' plot twist, it is revealed that Mary (Charlize Theron's character) was once married to Hancock and that she also is an invincible alien. She explains that when they are together, they lose their powers.
But this rule is raped beyond recognition when the two past lovers start fighting each other for no reason; flying around Los Angeles, destroying buildings and creating comically dark tornadoes.
Major Plot hole: Red Parker, the bank robber that Hancock puts in jail half-way through the film, escapes from Prison in order to fulfill is revenge against the superhero......by shooting him. What is interesting is that the audience knows that Hancock is now weaker because of his proximity with Mary, but Red Parker doesn't know that.
The only thing he knows so far, is that Hancock is invincible and strong enough to cut arms by simply throwing metal disks. But this information seems to be enough for him to do everything in his power to escape from prison and to shoot an invincible man that he knows can kill him in a mere second. Why ?
Plot contrivance: Instead of pushing Ray's car outside of the train tracks, Hancock saves Ray by putting himself in-between Ray's car and the advancing train, thus causing major destruction and the probable death of the train-driver.