If you still have your combat log, can you check to see if your pet was using its special attack (claw/bite/etc) during the fight? There was a bug (Blizz says it was fixed, though I am still seeing it with some of my pets) where pets were not using this ability, thus not building stacks of frenzy, so Focus Fire was hardly being used. Just wondering if that is the case here. Or do you recall if you were sitting at 5 stacks of Frenzy for long periods?
Currently Focus Fire should be cast when you are not under Beast Within or any Heroism/Rapid Fire type affect, and the cooldown for Bestial Wrath is > 30 seconds (and you have 5 stacks of Frenzy). I have been playing a lot with the waiting for Bestial Wrath cooldown bit, I read a lot of pros/cons for waiting, but in the sims I've built and run, it does seem to be a DPS increase. Of course, in the real world it might not work so well. If you are confident you are not having problems building stacks of Frenzy, you can try tweaking the wait time (search for "Spell.GetSpellCooldown("Bestial Wrath").Seconds > 30" in a file called "BeastMastery.cs" in your Pure directory) and see if that helps. I suppose that could become a user setting if others are interested...