Ability Scores
 

I have an animal companion, and his scores really suck, with my highest being +3 for dex. It even has -4 for Int, which is supposed to be around 2 or 3.

Yet, the program is acting as if these are the modifiers, with the scores themselves completely eliminated.

I am thinking that Dex should be at 16, not 3, though 3 would be the ability modifier. Is it not showing the actual ability scores? Why would these be excluded?

This sounds like the companion is being displayed as an NPC. I think PF2 has changed the NPCs/monsters to be much simpler to manage, so they've ditched the 3-18 stats since they don't achieve much compared to the actual stat bonuses.

Hello thaX,

Farling has the right idea here.

For PF2, Animal Companions actually don't possess Ability Scores directly, instead, they are represented with Ability Modifiers only. This is working 100% as intended and as the source material presents those rules. If you like, you can check the Rules for this on page 214 of the PF2 Core Rulebook.