It's not mentioned nor shown in the movie, but the Israelis destroyed several Ugandan MiGs on the ground of Entebbe airport, to keep the aircraft from being used against them, and as part of an agreement with the Kenyan government in exchange for allowing the raid aircraft to refuel in Kenya.
Lieutenant Colonel Yonatan "Yonni" Netanyahu was the older brother of Benjamin Netanyahu, Prime Minister of Israel since 2009. Both served in the Israeli Defense Forces and the elite commando unit Sayeret Matkal, which conducted this operation.
A lot of this movie was shot at Malta International Airport in Luqa. A day after filming wrapped in Malta, a real-life hijacked Libyan airplane landed very close to the set. The hijackers used replica hand grenades and pistols.
The film puts Yonatan Netanyahu's death much earlier in the raid on the airport than had been portrayed in previous films on the subject or in the Netanyahu family's version of events. Director Padilha said that this placement was based on interviews with participants in the raid.
StudioCanal optioned the rights to "Operation Thunderbolt: Flight 139 and the Raid on Entebbe Airport, the Most Audacious Hostage Rescue Mission in History" (published December 1, 2015), by Saul David. The book contains information that had previously not been available for books written about "Operation Thunderbolt".