I had similar issues with my original focus macros; the solution is sort-of simple: Remove /assist from JUST your Main's macro, leave it in everyone else's. The only problem with this is that should you change mains/focus mid-battle you'll run into the same /assist = targeting self issue.

The reason this happens, assuming I'm reading it right, and you're mid-fight, is because the MOB you're attacking has YOU targeted; /assist works on MOBS too. Mob targeting you = /assist with mob targeted = you targeting you. Got me killed a few times when I was starting out lol; once I removed /assist from my Main's macro though I had no more issues and my alts always targeted the right mob assuming I compensated for the Focus Update lag.

Edit: If this is out of combat then that's either normal if your main doesn't have a target, or if it does, you're either not waiting for Focus to update, or there's something wrong with your macros lol; post 'em if you can