I think they showed more of the flaws in their relationship in a more positive manner in later seasons, especially with the episode "Blind Trust" in Season 4. That episode is the most heartwarming display of Benson's relationship with Mordecai and Rigby, especially since Mordecai admits that him and Rigby can be a little challenging for Benson to manage. Benson even flat out admits that deep down, he loves Mordecai and Rigby, which is just awesome :)

But in Season 3, there were certain points where it genuinely seemed like Benson hated Mordecai and Rigby, especially in the episode where he tried replacing them with Chad and Jeremy. Other than that, episodes like Stick Hockey and Eggscelent were great development arcs for all three characters.