What is the irony of Johnny killing Bob?

The irony here is that gentle Johnny Cade is the last person on earth you'd expect to kill someone in a fight. Johnny's normally such a quiet, passive soul, and although he's always showed great physical bravery, he's also been something of a peacemaker. Yet now he's a killer. He may have acted to save Ponyboy's life, but he's a killer all the same.
What's interesting is that Johnny's saving of Ponyboy's life parallels what happens later on in the story when he sacrifices himself to save the lives of children from a burning church. There's more than an element of Christian symbolism here. Johnny has to go through the flames to purge himself of the sins he's incurred by killing Bob. Fire is both a symbol of destruction—it ends Johnny's life—and rebirth—Johnny is redeemed by his final selfless act of bravery.

Irony is a literary term that applies to situations in literature where there is a strong incongruity between what is expected to happen and what actually happens. Johnny Cade, the murderer of Bob, is characterized as a "dark little puppy," vulnerable and prone to suicidal thoughts as a result of being abused by his parents and physically beaten by the Socs. He is kind and thoughtful to his friends, and Ponyboy sees him as a sensitive soul who desperately needs the emotional support of the gang of Greasers. Because Johnny is described as a somewhat weak and passive character, he is the least likely of all the Greasers to be a violent killer. Johnny's personality characteristics and his background as a victim of others' abuse combine to make his murder of Bob ironic.