It wasn't an "accident" because they intentionally targeted the ship. They just misidentified it.

Very long story short: the Israeli Navy misidentified the boat as Egyptian. The pilots were designated to target the boat, were even concerned that it could have been American (they couldn't see the flag from the altitude that they were at), and their mission was already to target almost anything that moved in Egypt. So they lit it up with several gun runs until it became clear that it was an American ship and the Israeli navy had completely fucked up.

The Israelis actually did try to help the ship afterwards but because the liberty was a) a spy ship, and b) just been attacked by the Israelis, they didn't let them help and returned to the fleet.

It's not like friendly fire can't happen. This kind of shit happens a lot more than people want to believe. There's a reason more people died in the Gulf War from friendly fire, than from enemy fire.