Next time use a better strategy when adding new skills to your pet. Imagine like this: Your pet has 3 slots of skills (1, 2 and 3) and you put novice magic and it goes to slot 3. Now you put novice magic and it goes to slot 1. Your pet will have 33.33% of chance of learning the 3rd skill without overwriting the others. BUT, if you put a Standard Magic before having the 3 skills, for example, it will replace the Novice Magic. But there's will still have one slot available for the third skill, and you have the same chance either for replacing that Standard skill and for having success on getting all the 3 skills.
Summing up:
Try to always get 3 novice skills before getting 1 standard.