Per page 131, Animal Companion's Instinct is a stat that has only negative effects.
You choose as many weaknesses as the Instinct score, and when someone else interferes with you trying to Command the animal, the interfering player adds the animal's Instinct to the interfere roll. So relative to the baseline stats you've factored out, there are 3 benefits (extra +2 Ferocity, armor 1) and 1 detriment (extra +1 Instinct), balancing out to the same 2 extra benefits as the others.