Animals with less than 3 INT cannot put skill points in non-animal skills. PCGen currently allows this.
Also Escape Artist, Intimidate and Survival should not be class skills. In PCGen they currently are.
Core Rulebook page 53:
Animal companions can have ranks in any of the following
skills: Acrobatics* (Dex), Climb* (Str), Escape Artist (Dex),
Fly* (Dex), Intimidate (Cha), Perception* (Wis), Stealth*
(Dex), Survival (Wis), and Swim* (Str). All of the skills
marked with an are class skills for animal companions.
Animal companions with an Intelligence of 3 or higher
can put ranks into any skill."
Due to the state of the Pathfinder Set (Major overhaul) I can't easily get the updated files to you without risk of breaking your version of PCGen.