The attack on (and sinking of) USS Panay (which had US flags painted on its deckhouse & deck), along with the sinking of 3 US-flagged tankers evacuating civilians from Nanking, by Japanese Navy aircraft on 12 December 1937?
The Japanese insisted it had been a mistake and paid reparations, but U.S. Navy cryptographers had intercepted and decrypted traffic relating to the attacking planes which clearly indicated that they were under orders during the attack, and that it had not been a mistake of any kind.
This information, along with the movie film footage which showed the US flags painted on Panay, were suppressed by the US government to avoid a public outcry that might lead to being forced into military action against the Japanese.