Keep in mind that the system, as written, is incredibly robust and balanced. If you use the published Fantasy Craft material, without house rules, nothing will break. Crafty deserves some serious cudos for this achievement.
If your group starts manipulating things - changing the feat types as Rhishisikk mentioned, or allowing players to take multiple Animal Partners / Personal Lieutennants, things may indeed go wonky. Sheena-Tiger, you mentioned that your group uses a rule about allowing multiple NPC feats of the same type (and I assume you game with Bhurano) - this may very well unbalance the game, especially with things like Path of Beasts and Beastmaster in the mix. You should also note in the rules as they are, the only way to get a second Animal Partner feat that I can recall is the Lancer's Core Ability - a big cost as you only ever get a max of 2 Core Abilities, so it will define a character. Honestly, if my GM said I could take 2 Personal Lieutennants or 2 Animal Partners, I would almost never decline - that right there is evidence of a balance issue.
Like I said, my previous games have had some serious NPC use (everyone with a minimum of 1), and my group are massive power gamers (we knew exactly what the errata would be because it's stuff we saw as having abuse potential). So far the only problem we had with pets was the Coordinated Strike chain, and after everyone who GMs collectively said "no" to that one, NPCs were no longer a problem. Stick with the RAW and you'll have no problems.