I think the differences with the helicopter incidents are obvious; they are smaller and faster by far than the ship.
But relative to a fighter jet their speeds are both extremely slow. And as mentioned Blackhawk helicopters are exclusively used by the US (at least in Iraq) and they are clearly identified. Still didn’t stop them being shot down.
Again what about the multiple recon. flights before the attack?
The multiple recon flights identified the ship as the Liberty. However the fatal error seems to have been the following (taken from Michael Oren’s article, a copy which I have found online)
"At 1:41 p.m., Ensign Aharon Yifrah, combat information officer aboard the flagship of these torpedo boats, T-204, informed its captain, Cmdr. Moshe Oren,23 that an unidentified ship had been sighted northeast of El-Arish at a range of 22 miles. The ship was sailing toward Egypt at a speed, Yifrah estimated, of 30 knots.
Yifrah’s assessment, twice recalculated and confirmed by him, was pivotal. It meant that the ship could not be the Liberty, whose maximum speed was 18 knots. Moreover, the Israelis had standing orders to fire on any unknown vessel in the area sailing at over 20 knots, a speed which, at that time, could only be attained by fighting ships. This information, when added to the ship’s direction, indicated that the target was an enemy destroyer fleeing toward port after having shelled El-Arish.
The torpedo boats gave chase, but even at their maximum speed of 36 knots, they did not expect to overtake their target before it reached Egypt. Rahav therefore alerted the air force, and two Mirage III fighters were diverted from the Suez Canal, northeast to the sea. When they arrived, the vessel they saw was “gray with two guns in the forecastle, a mast and funnel.” Making two passes at 3,000 feet, formation commander Capt. Spector (IDF records do not provide pilots’ first names) reckoned that the ship was a “Z” or Hunt-class destroyer without the deck markings (a white cross on a red background) of the Israeli navy. Spector then spoke with air force commander Gen. Motti Hod, who asked him repeatedly whether he could see a flag. The answer was “Negative.” Nor were there any distinguishing marks other than some “black letters” painted on the hull.
IAF Intelligence Chief Col. Yeshayahu Bareket also claimed to have contacted American Naval Attaché Castle at this point in an attempt to ascertain whether the suspect ship was the Liberty, but the latter professed no knowledge of the Liberty’s schedule - a claim later denied by Castle but, strangely, confirmed by McGonagle.24 One fact is clear, however: After two low sweeps by the lead plane, at 1:58 p.m., the Mirages were cleared to attack."
So the ship was identified earlier, but due to miscalculations of speed it was determined the ship spotted later was not the USS Liberty, and seeing that the Israeli Army/Navy was under orders to fire on any unidentified ship the attack was ordered.
The Israeli pilots could have identified the ship was American without a flag. (from the markings, equipment etc.)
But they didn’t have to, nor was it their responsibility. The ship had already been marked as not being the Liberty (due to the speed miscalculation), the pilots checked to see if they could see a flag (which they reported that they couldn’t, which has been confirmed by both the tapes the IDF released and from other sources such as Nowicki) and seeing that the ship was going to fast too be the USS Liberty it was assumed to be Egyptian and attacked.
As for the distinctiveness of the equipment on the Liberty it obviously wasn’t distinctive enough as the pilots reported it as being “gray with two guns in the forecastle, a mast and funnel.”. Hardly a distinctive description.