Often! Whenever you can!
Poor bunny. Happy reader!
Every scene has three parts: goal, conflict, disaster. You can hurt your bunny during the conflict part; that's obvious. he has to fight a bully, scale a mountain, or survive a hurricane. You can also hurt your bunny during the disaster. That, too, is obvious. A bomb goes off, the boogie man jumps out of the closet, he gets a huge pimple on his nose just before his big date with the head cheerleader. Youch!
Every sequel has three parts: reaction, dilemma, decision. You can also hurt your bunny during the dilemma, as he tries to decide what to do. That, again, is obvious. You can make him agonize over what to do. Does he pull the plug on his brain-dead son? Does he confront the bully? Does he run into the burning building to save the child?
You can hurt your bunny as soon as he's made a decision about what to do. How? Make that decision a poor one. Perhaps he's made the choice to have it out, once and for all, with the fellow employee who is always stabbing him in the back. But, perhaps, that choice is the wrong one because he doesn't know yet that he doesn't have all the correct information, and it's the wrong fellow employee being accused. Perhaps the information he's using is out of date, so the choice to not vaccinate his child is based on incorrect data. Perhaps he assumes the head cheerleader won't mind the huge pimple and will like him for who he is inside.
What about hurting your bunny during the goal? Perhaps your bunny in the previous sequel has made a decision about what to do next. His goal now for the next scene is to implement that decision. So how do you hurt him? By allowing him to have the wrong goal. What follows will hurt him. He's decided to confront the bully, which is a good decision, but his goal to do it during lunchtime when the bully's friends are there to help him, is a bad idea.
You get the idea. Hurt your bunny often. Chase him up a tree and throw rocks at him. Remember, though, that your bunny must grow stronger during each time of "hurt." You're hitting him with his weaknesses, his flaws, his fears. As he works out how to survive each onslaught, he gets a little stronger. So, by the end of the book, your bunny has grown as a person, has grown into a stronger, wiser rabbit. What didn't kill him will make him stronger. And at the end he can dance with the giant carrot. Or maybe eat it