Yes, like Andy said, they will still breed with each other, it will just take a little bit longer to get an egg when you get that message, as opposed to getting a message that says that the Pokémon are friendly or like each other. Pokémon will breed a little faster if they have different trainers. (Basically, what I mean is that if you breed two Pokémon where one was caught by you in your game, and the other was traded to you, either from another version or through an in-game trade, then you will get an egg faster then you would by breeding two Pokémon that have the same original trainers.) In all reality though, the difference really isn't that huge. No matter what, sometimes it seems like it takes forever to get an egg, and sometimes you will get an egg in a couple of minutes.