I also wondered why Ferris didn't take Kensi when he visited. Although, maybe they were going to try to have Kensi ponder cheating on Deeks with him and though against it because it would make her look like crap and decided to make him a bad guy. Or they wrote it that way to make Kensi trust Sullivan, but as an agent with tradecraft, she should not let relative strangers in her home, let alone tell people where she lives (plot holes).
Maybe they had Deeks arrested, knowing that Kensi would eventually visit him. The bad guys did this in a second season episode (can't remember title) , where they shot Deeks (because he had such bad tradecraft and let people become aware of his routines) and waited for Kensi to leave the hospital to attack her.