If Gondwana was a whole continent, why did some animals go with Africa, some with Asia, some with Australia, etc?
Within a continent, especially one as large as Gondwana, different animals live in different environments. Imagine if Australia broke up today – you would find Fairy Penguins only in the part that had been Victoria, and Tasmania, you would find crocodiles only in the parts that had been North Queensland, Nth NT, and Nth WA, and you would only find Jarrah trees in the part that had been the South of WA.