Literally one of my favorite thing is when two characters are fighting for the same goal but their morals and/or way of approaching the problem differ. Sorta like the example, where both characters want to stop the "bad guy" just that their focuses are different.
Or another example where two characters both want to protect their city from an evil government, but A wants to kill all the people involved and completely remake their society while B believes they should infiltrate the government and make change from the inside. They both have the same goal but because of their differing methods, there may come a time where they have to disobey each others orders. Leading to betrayal. Maybe B is at a government meeting and A ends up destroying things there even after B telling them not too. Betrayal, but in a way they're both doing what they think is right for the given situation.