I've got the exact same problem. And after unlocking Mecha-Naruto you would probably still have 1% or 2% left to complete. I've got 97% only on tasks, rest is 100% and I can't find what I'm missing.
Do you have unlocked Nagato, Konan and Pain? Because somehow I didn't unlock them even after Konan's task. Though I played as Pain, so it might have bugged or some...