There is one incident that comes to mind: The Laconia Incident. When the hospital vessel Laconia was sunk by a German U-boat, the U-boat's captain realized the mistake and took on the survivors on its outer hull and lashed the lifeboats to the submarine, and radioed his superiors to ask their support in carrying out a rescue. He put a Red Cross flag up and draped his boat in a second flag. Three other U-boats arrived to help with the rescue and hopefully bring the survivors to Africa where they would rendezvous with Vichy French warships to bring them to where they could receive care. All three flew red cross flags.

An American B-24 bomber spotted the three-boat formation and the flags. The U-boat crew signalled for help, and the survivors waved from the hull. The B-24 crew radioed to base for orders and described the situation - the order was to attack. The U-boats were bombed and were forced to submerge, abandoning their survivors to the ocean. After that, the Kriegsmarine forbade any rescue attempts of victims of submarine attack, perhaps fueling later media depictions of U-boat crews abandoning or attacking survivors. Not helping matters was that Donitz ended up getting tried and convicted for 11 years for issuing that order, further fueling the postwar rumors that German submarine crews were supposedly merciless.

Legally, the red cross flag offers no protection for a military vessel or formation under the Geneva convention. It is only illegal to attack a place or vehicle or person designated with a red cross if they are not armed or carrying a weapon - as soon as they're armed, they're no longer protected. The B-24 did not commit a war crime by attacking. To this end, military forces generally don't like doing this as it relies entirely upon your enemy not taking advantage of you, which they are well within their rights to do under the law. It's screwed up.