So long as they’re well-trained and well-fed, no, not at all. Predator and prey pokémon typically have no trouble getting along on the same team so long as they understand that their minimum needs will be met and that they’re meant to work together as a team.
Of course, keep in mind that you will need to actively teach your pokémon both of these things, as we’re talking about a behavior modification. You will essentially need to train your pokémon to understand that they’re no longer in the wild, and this can be as easy as establishing and following a routine. Feed your pokémon every day at the exact same time so they can know that they have a daily source of food, and the rest should be easy.
Granted, should your pokémon display animosity towards each other anyway, even after you train them to know when they’ll be fed, you’ll need to consider it a form of interpersonal hostility, determine the exact source of your pokémon’s disagreements, and work towards making both sides feel more relaxed towards one another. The tips outlined in this post should provide further help in that matter: http://bills-pokedex.tumblr.com/post/165308388176/my-umbreon-and-charizard-will-not-stop-arguing
The Pokédex According to Bill 