As far as I know, all the similarities mentioned are just coincidence. These words are in Indonesian and Malay long before Indonesia come into significant contact with Japan.
It's possible that these similarities may come from Sanskrit, which Indonesia and Japan both take cultural influences from, due to the spread of Buddhism. But I don't think I know the employee's etymology of either language enough to actually declare that connection.
Could someone please explain why "I like the apple" was marked incorrect? In the tips and notes section of this lesson, it says that 'Saya mau apel' could mean either "I want apples" or "I want an apple". Why doesn't that theory apply to this sentence? I feel like I'm missing something really obvious.