1. The Tantura massacre
Israeli journalist Amir Gilat published an article regarding a massacre in Tantura in Ma’ariv which was mainly based on a master’s thesis submitted to the University of Haifa by graduate student, Theodore Katz. In a paper on The Exodus of the Arabs from the Villages at the foot of Mount Carmel, Katz said Israeli forces killed 240 Arabs from Tantura during the 1947–1949 Palestine war in 1948.
Having discovered they were publicly accused of war crimes in the pages of Israel’s largest newspaper, veterans of the 33rd battalion of the Alexandroni Brigade were outraged. They maintained that the battle for Tantura was a strategic one, an attempt to stop the maritime smuggling of arms and food and to prevent the Haifa-Tel Aviv road from being cut off; and that throughout the fight for survival in a bloody war launched by the Arabs, they had maintained the strictest ethical standards. While the battle for Tantura was difficult — 14 members of the IDF battalion and about 40 Arabs were killed in street fighting — the veterans insisted Katz had lied about a massacre. 
At the end of the legal process, which Katz paid for with Palestinian Authority funding, he was compelled to publish at his own expense newspaper advertisements in which he completely repudiated the massacre lies, eliminating any possibility of generously referring to them as a “contentious version.” Katz’s ads stated:
After checking and re-checking the evidence, I am now certain beyond any doubt that there is no basis at all for the allegation that after Tantura surrendered, there was any killing of residents by the Alexandroni Brigade, or any other fighting unit of the IDF. I would like to clarify that what I wrote was misunderstood, and that I did not mean to suggest that there had been a massacre in Tantura, nor do I believe that there ever was a massacre at Tantura.
2. Mass execution of Egyptian POWs in El Arish
Not content with these long-refuted myths, Norman Finkelstein invokes:
“unimpeachable eye-witness testimonies of Israeli soldiers, as well as the testimony of an Israeli military historian, that the IDF executed scores of Egyptian POWs during the June War.”
No further evidence is given, but his footnote cites press reports on the testimony of “eye-witness” Gabi Bron and “military historian” Aryeh Yitzhaki. Both sources had explicitly disavowed the statements attributed to them as media inventions. Egyptian POWs “were not shot, and there were no mass murders,” asserted Bron. “In fact, we helped prisoners, gave them water, and in most cases just sent them in the direction of the [Suez] Canal.” Yitzhaki, who was not a military historian but a clerk in a military archive, was even more emphatic: “In no case did Israel initiate massacres,” he wrote. “On the contrary, it did everything it could to prevent them.” The specific examples mentioned in Finkelstein’s reports proved to be legitimate acts of war; thus an alleged mass killing of hundreds of POWs at El-Arish in the Sinai turned out to be a battle with enemy forces who attacked an Israeli convoy. And all of this was known years before Finkelstein chose to repeat the allegations. The conclusions would seem to be obvious. 
3. Lydda Massacre
“Lydda, 1948” (The New Yorker, October 21, 2013) written by the well-known and talented Israeli journalist Ari Shavit. In Shavit’s very deceptive and even contradictory recounting, Israeli soldiers led by a certain Lt. Col. Moshe Dayan, and armed with:
a giant armored vehicle mounted with a cannon, menacing half-tracks, and machine-gun-equipped jeeps
joined other Israeli forces attacking Lydda (and its neighbor Ramle) during Israel’s War of Independence. Led by Dayan’s marauding forces the Israelis took control of “key positions” in the town, but the next day fighting flared again, and:
in thirty minutes, two hundred and fifty Palestinians were killed. Zionism had carried out a massacre in the city of Lydda.
Is this really what happened?
The overall commander of the operation in Lydda, Moshe Kelman, met with the town’s leaders to discuss surrender terms, beginning with Simon Garfeh, the Greek Orthodox Archimandrite of Lydda. Garfeh gave the following account, as recorded by historian Dan Kurzman:
“I am the Archimandrite of Lydda,” he announced. “I hope you have come in peace.”
“If it is the desire of the people of this town to live with us in peace,” Kelman assured him, we shall be very happy.” They may open their shops and resume normal life. Can you arrange for the surrender?”
“I shall try,” the prelate answered … “I shall ask the leaders of the Moslem and Christian communities to meet with us immediately in my apartment upstairs.”
He then instructed an aide to run to the Big Mosque to fetch the Moslem leaders, and sent another to his own church to bring the Christian leaders taking refuge there.
About an hour later, a dozen Arab notables were sitting in Garfeh’s living room sipping coffee and chatting with the clergyman, Kelman, and other Israeli officers. Finally, Kelman, putting down his coffee, addressed them:
“Gentlemen, the city has been conquered, and we want your cooperation. We suggest that you find the citizens who have been operating the utilities so that your people can have water and electricity without delay. But first you must accept our terms for peace: Surrender of all fighting personnel and of all arms within twenty-four hours. If these conditions are not met, we shall have to take action.”
“We agree,” one of the Arabs said with quiet resignation. “May the residents stay here if they wish?”
“Yes, they may,” Kelman replied, “if they live here peacefully.” (Genesis 1948, Dan Kurzman, p. 514)
Shockingly, Shavit gives no hint of this. Why would Shavit and his editors omit the crucial fact that Lydda had surrendered, and had agreed to disarm and live in peace, and that the Israelis had agreed to let them stay? Why would Shavit and the renowned New Yorker “fact checkers” ignore Kurzman’s crucial interviews?
Shavit also keeps from his readers the fact that the hard-pressed Israelis withdrew a significant part of their forces from Lydda after the surrender, since they were needed elsewhere. Dayan’s battalion, for example, headed south, to take part in the battle for the Negev. (Moshe Dayan, Story of My Life, p. 112)
The very next day, July 11, the Jordanians sent a patrol to the outskirts of the town, made up of one tank and two armored cars, to probe Israeli strength. Shavit mentions this — he says it was “two Jordanian armored vehicles.”
But for some reason he doesn’t call them “giant armored vehicles,” or “menacing.” Perhaps only Israelis have giant armored menacing vehicles.
Shavit does say that the “two vehicles were of no military significance.” So one of these vehicles in Israeli hands was of great significance, but two in Jordanian hands were, for some reason, irrelevant.
the explanation for these contradictions, the Jordanian patrol ran into trouble, and had to shoot its way out of town. The residents, apparently thinking this was a Jordanian assault to retake the town, began attacking the remaining Israeli soldiers. Five Israeli guards stationed outside the Dahmash Mosque were the first to be killed, and almost immediately the entire town erupted in shooting. (Kurzman, p. 515)
Despite the surrender agreement, and the promise to turn over arms, the Israelis, now numbering only 500 men, had to once again take the town in another desperate battle.
Fighting house-to-house to root out snipers, and this time giving no quarter, within an hour much of the town was once again under control, and an estimated 200 Arabs were dead.
But the Dahmash Mosque, was still fighting, held by an estimated 70 fighters, and with an unknown number of others inside. Rather than launch a costly frontal assault, Lt. Col. Kelman decided to breach the mosque’s walls with an anti-tank weapon, known as a PIAT, and then have a platoon rush the building.
After the PIAT was fired, the men that stormed the building found that the defenders were dead, killed by the effects of the armor piercing projectile in the confined space of the mosque. (Kurzman, p. 515–516)
The second battle to take Lydda was over, but now facing the Israelis was the difficult question of what to do with the inhabitants. The town leaders, knowing that they had broken their word to surrender and disarm, and knowing in particular that the five Israeli soldiers outside the mosque had been massacred and their bodies mutilated, feared that the Israelis would now return the favor.
It’s hardly surprising that the Israelis were in no mood to give the residents another chance to break their promise to live in peace. But, of course, the Israelis also didn’t execute or “massacre” them. Instead, the residents were ordered to evacuate the city and move towards the Jordanian lines and Ramallah. 
4. Jenin massacre
Among the most disputed and misrepresented facts about the fighting in Jenin was the number of Palestinians killed and the extent of the destruction. Initially, Palestinian officials claimed that hundreds were killed in the “Jenin massacre.” For example, then Palestinian Authority Minister of Local Government Saeb Erekat stated on CNN April 10, one week into the eight day operation: “I’m afraid to say that the number of Palestinian dead in the Israeli attacks have reached more than 500 now.” (See the Backgrounder in CAMERA On Campus Fall 2002 for an in-depth review of PA misinformation.) Later, when international workers investigated the camp and found no evidence of a massacre, Palestinian officials drastically lowered the death toll to 56, a number consistent with what Israel had estimated (Washington Times, May 1). 
5. Deir Yassin
For many decades the number of victims were believed to be around 250, based on Raanan’s false estimate. Modern scholarship puts the number at about half that. Sharif Kan’ana of Bir Zeit University interviewed survivors and published figures in 1988; 107 villagers had died, 11 of them armed, with 12 wounded. Israeli researcher Eliezer Tauber writes that a total of 101 people were killed, 61 definitely in combat circumstances (including 24 armed fighters, with the remained being their family members who were with them); 18 for whom the cause of death could not be determined; about 10 whose deaths are in a “grey zone” whose charactization can be debated; and a further 11 being members of a single family who were gunned down by a single Irgun member.
 The Jewish Divide Over by Paul Bogdanor pg 142