The talent Animal Companion does not interact with other stable slots, only the first one.
In short:
If you pick Animal Companion as a talent, when you then at some point call one of your active pets(of which you can have a total of 5 different ones at any point), Animal Companion will then proceed to also call the pet you have placed in the first stable slot in your stables.
Active pets = go into their own slots, and can be called from anywhere in the world. You can change what pets you have as active pets by talking to a stable master in a city, by opening your stables and by default you then have the active pet slots on the left side of the interface panel in a vertical line.
Inactive pets = stabled pets. These you cannot interact with in any way unless you visit and talk to a stable master in a city. The stabled/inactive pets are found in your stables when you talk to a stable master, they are located at the bottom/bottom right side of the interface panel in a grid-like pattern. The interface shows 10 of your stabled pets per page, for a total of 20 pages(200 pets).
Feel free to check out this link below here. Perhaps there’s something new in there that you don’t already know^^