Sam: I think I tore a ligament or something jumping onto that bus.
Jesse: My god, would you stop complaining about that?
Sam: I'm not complaining! It just hurts!
Sam is complaining to Jesse and limping because he hurt his ankle. When Burke calls and tells them to go back and kidnap one of the Agents, Sam's injury disappears. He manages to sneak up and toss the guy into the trunk of a car.