Our evil game just started. There are four players. Three sessions in, and some conflict is already brewing. However, it's not because of evil alignments. It's because of stupid actions.
One player has a tendancy to make choices that are very amusing to him, but not contributive to the group. Things like hiding his abilities and plot knowledge from the party when that information would be useful for everyone to know. Or taking actions in combat that he thinks are hilarious, but don't actually help defeat the encounter. Then there're the arguments out of combat that slow down play and a dozen other aggravations.
Thing is, none of this is because we're playing an evil game. This player does the same sort of stuff all the time. In fact, the whole group is interacting with each other in pretty much the same way as we always do. The only difference is that now the only reason I haven't tried to kill him yet is because I don't know if I can take him without getting killed myself. Usually I don't attack him because it would cause party tension and it's wrong to attack companions.
When it comes down to it, the characters are the evil ones, not the players. But the players are going to be the ones that make or break the game, because they are going to be making the decisions that either make a cohesive group that has adventures and makes stories, or if they're going to bicker.
When your players are making characters, it's ok to tell them what's acceptable in your game and what's not. Tell them to make choices that will result in a group that will work together. Once your troublesome player makes a character who will want to backstab and kill the party, it will be very hard to avoid the "I'm just playing my character!" syndrome.
Remember the golden rule: I will not allow my fun to come at the expense of anyone else's fun.