The Mossad certainly played a role in the 1967 war, but it is not responsible for controlling Israeli combat aircraft and recording their conversations with ground command.
If flags and ships are always easily identifiable from the air, what accounts for the sinkings from 1940, 1944, and 1974 that I’ve mentioned (plus all the other mistaken attacks I haven’t cited)? While I don’t think the Israeli pilots were stupid (one of the men involved was credited with 13 air-to-air kills during his flying career), I also think ship recognition drills weren’t high on their priorities. (Another case: in 1941 an entire formation of British carrier aircraft mistakenly attacked the cruiser HMS Sheffield while it was shadowing the German battleship Bismarck. The aircraft came from a carrier that had been operating in the same task force as the Sheffield for over six months.)
The Liberty hadn’t been spying on Israel regularly. It had been converted into a spy ship in 1965 and spent the next two years operating off West Africa. In May 1967 it was sent to the eastern Mediterranean for the first time. The Israelis IDed her correctly early on the morning of June 8, but when the ship was spotted again shortly before noon, the IDF mistakenly believed the Liberty had left the area. ‘Fog of war,’ the same fog that prevented the Liberty from receiving in time message sent from Washington telling it to move 100 miles off the Sinai coast.