In a blog post, Wolfire's Jeffrey Rosen says the team wants to provide for those who bought the illegitimate copy. "If you accidentally purchased the fake Lugaru, you can forward your receipt to [Wolfire] and we will give you an authentic version of Lugaru HD, as well as a bonus Steam key for your trouble."
As for how the clone was yanked, the team at Wolfire seems stumped. They haven't heard back from Apple and are unsure what prompted the removal. Alex Matlin of iCoder, the company responsible for the clone, told Kotaku that it "was removed from sale by the development team," but didn't elaborate. We sent out word to iCoder for clarification, but haven't heard back.