The problem in Divergent was that the Erudite injected all of the Dauntless and while the Dauntless thought they were sleeping they were actually being controlled by the Erudite. The Dauntless didn't know that they were killing the Abnegation.

Beatrice and Tobias resolved this problem. They were Divergent so they were awake and they got past Jeanine and stopped the systems. Then all of the Dauntless woke up and realized what they have done.

Problem and Resolution