Prosecutors were able to obtain the encrypted chats because, as Motherboard notes, Manafort was backing up information from his WhatsApp to Apples iCloud, where data is not encrypted and is thus available to police armed with a valid search warrant.That says that he was foolishly not using Apple's encryption. Either there's something wrong with that descriptionl or Manafort was stupidly storing stuff in an unencrypted form.
Even Apple can't stop a determined user from doing something stupid.
If I'm mistaken in my reading of this situation, I'm sure Swordmaker can correct me with regard to Apple's involvement. It seems counter to everything I have read about Apple's encryption.
It appears to me you have to try to do so, since local backup through iTunes -is- privately encrypted, and that's the recommended way to do it.
So Manafort chose to backup his phone messages without private encryption. Stupid.
Apparently Manafort did not set the encryption for his backup of the WhatsApp data. As you said, Apple cannot protect users from themselves. Apple especially cannot protect users from developers who neglect to turn on the encryption API by default for their Apps, which I thinks makes this a failing of WhatsApp.