The Spawn Combatants step has to be after loading the new scene, else the combatants would be spawned in the old scene and destroyed when loading the new scene.
Maybe it'd be best to send me your battle start event and I'll take a look at what's going on: contact@orkframework.com
You can also set player group members to be AI Controlled - the setting can be found in the AI Settings of the combatant.
If you're adding your pats as group members or as an allied group depends on how you want them to be implemented in your game. As group members, they'd also be visible (and accessible) in menus. As allies, you can simply spawn them at the start of the battle and remove them afterwards - but their statuses wouldn't be kept for the next battle, so it'd always be a new pet.