[DahkCeles]

Option 1: Add a safeguard to RecordPet() so that it doesn't try to execute when information is missing.

function BattleDex.RecordPet(species, level, quality, primary)
    if (species) then
        --print(string.format("s=%d, l=%d, q=%d, p=%d", species, level, quality, primary));
 
        _G.BattleDexDB.pets[species] = _G.BattleDexDB.pets[species] or {};
 
        local key = primary.."_"..level.."_"..quality;
 
        _G.BattleDexDB.pets[species][key] = _G.BattleDexDB.pets[species][key] or 0;
        _G.BattleDexDB.pets[species][key] = _G.BattleDexDB.pets[species][key] + 1;
    end
end

Option 2: Change RecordBattle() so it is smart enough to know you sometimes have fewer than three pets.

I think you can do it using C_PetBattles.GetNumPets() but its probably also doable with a simple if (s2) then ... end

function BattleDex.RecordBattle()
 
    if (not C_PetBattles.IsWildBattle()) then
        return;
    end
 
    -- first pet
    local s1 = C_PetBattles.GetPetSpeciesID(2, 1);
    local l1 = C_PetBattles.GetLevel(2, 1);
    local r1 = C_PetBattles.GetBreedQuality(2, 1);
    BattleDex.RecordPet(s1, l1, r1, 0); -- 4th arg means self is primary
    
    -- second pet
    if (C_PetBattles.GetNumPets(2) >= 2) then
        local s2 = C_PetBattles.GetPetSpeciesID(2, 2);
        local l2 = C_PetBattles.GetLevel(2, 2);     
        local r2 = C_PetBattles.GetBreedQuality(2, 2);
        BattleDex.RecordPet(s2, l2, r2, s1);    -- 4th arg points to first pet
    end
    
    -- third pet
    if (C_PetBattles.GetNumPets(2) >= 3) then
        local s3 = C_PetBattles.GetPetSpeciesID(2, 3);
        local l3 = C_PetBattles.GetLevel(2, 3);
        local r3 = C_PetBattles.GetBreedQuality(2, 3);  
        BattleDex.RecordPet(s3, l3, r3, s1);    -- 4th arg points to first pet
    end
end