I had understood that MtGOX was forced to file for bankruptcy protection because many clients were already suing it or were about to do so. The Japanese court easily concluded that MtGOX could never recover from such big losses, even after Mark found the 220'000 BTC that he had "forgotten about", so it determined liquidation.
Courts rarely do their own investigations, but rather rely upon information the parties before it present. If the Tokyo court was told 850K btc were missing, but the company only had 220k btc, then their ruling sounds reasonable. However, if the court was hoaxed too, and there were really never 850k btc, but only 220k, then their conclusion may have been unintentionally wrong. However, fractional reserves are not illegal, and as long as depositor's demands for withdrawals are met, then there is no reason to declare bankruptcy nor for the court to compel one.