According to the United States, Vincennes's crew misidentified the aircraft as an F-14 Tomcat, a US-made fighter jet part of the Iranian inventory, despite it transmitting civilian identification codes.

Some analysts blamed the overly aggressive attitude of Vincennes's captain, William C. Rogers III, while others focused on more widespread issues and miscommunications on board.

[1] In 1987, a year preceding the shootdown, the Iraqi Air Force had attacked the US Navy frigate USS Stark, killing 37 American sailors, after misidentifying it as an Iranian warship.

[2] After a US oil tanker struck a mine in the Persian Gulf, additional warships were dispatched to the area; by late 1987, US forces had challenged and launched missiles at two Iranian fighter jets.

[3] In April 1988, the US engaged in Operation Praying Mantis in retaliation for mines,[4] bringing significant damage to Iranian oil infrastructure and its military.

[5] In response to the pattern of attacks on shipping, the U.S. Joint Chiefs of Staff issued a 'Notice to Airmen' (NOTAM) on 8 September 1987, warning all Persian Gulf countries that civilian aircraft must monitor the International Air Distress frequencies and be prepared to identify themselves to U.S. Navy ships and state their intentions;[6] Iran disputed the validity and accuracy of these notices.

The Aegis system was capable of tracking multiple mobile targets simultaneously, both naval and airborne, and more importantly allowed rapid dissemination of information between different levels of the crew.

During the Iran–Iraq War the Iranian forces frequently boarded and inspected neutral cargo ships in the Strait of Hormuz in search of contraband destined for Iraq.

A helicopter deployed from the cruiser reportedly received small arms fire from Iranian patrol vessels as it observed from high altitude.

Vincennes moved to engage the vessels, in the course of which they all violated Omani waters and left after being challenged and ordered to leave by a Royal Navy of Oman warship.

[27] The location of Vincennes in Iranian territorial waters at the time of the incident was admitted by the US government in legal briefs and publicly by Chairman of the Joint Chiefs of Staff, Admiral William J. Crowe, on Nightline.

[30] Flight 655's crew, however, would have seen a speed of 300 knots (560 km/h; 350 mph) on their cockpit instruments, which was their indicated airspeed, possibly leading them to conclude that Vincennes was talking to another aircraft.

The ICAO concluded that Flight 655's crew assumed the three calls they received before the missiles struck must have been directed at an Iranian P-3 Orion which was also taking off from Bandar Abbas.

[34] In its ICJ statement, Iran disputed this by claiming that the Department of Defense's report explicitly mentioned the Vincennes' VHF radio equipment that would have allowed it to monitor civilian air traffic control frequencies, as well as other US surveillance activities in the Persian Gulf region that would have alerted them of the aircraft's nature.

Flight 655 was erroneously tagged by an operator with this military classification, possibly leading the crew of Vincennes to believe the airliner was an Iranian F-14 Tomcat.

[45] In 1990, investigative journalist Roger Charles, writing for Newsweek, obtained a full copy of the DoD's internal report which included a map and coordinates of Vincennes.

[46] The Fogarty report stated, "The data from USS Vincennes' tapes, information from USS Sides and reliable intelligence information, corroborate the fact that [Iran Air Flight 655] was on a normal commercial air flight plan profile, in the assigned airway, squawking Mode III 6760, on a continuous ascent in altitude from takeoff at Bandar Abbas to shoot-down.".

[47][48] The Fogarty report also claimed, "Iran must share the responsibility for the tragedy by hazarding one of their civilian airliners by allowing it to fly a relatively low altitude air route in close proximity to hostilities that had been ongoing.

[51] When questioned in a 2000 BBC documentary, the US government stated in a written answer that they believed the incident may have been caused by a simultaneous psychological condition among the eighteen bridge crew of Vincennes, called "scenario fulfillment", which is said to occur when people are under pressure.

[55] The US had previously issued a Notice to Airmen (NOTAM), warning aircraft that they were at risk of "defensive measures" if they had not been cleared from a regional airport and if they came within 5 nautical miles (9.3 km; 5.8 mi) of a warship at an altitude of less than 2,000 feet (610 m).

[63] Speaking to the United Nations Security Council, Ali Akbar Velayati, Iran's Minister of Foreign Affairs, called the shootdown the "most inhuman military attack in the history of civil aviation", caused by a "reckless and incompetent naval force".

[28] The Newsweek article also accused the US government of a cover-up;[69] Admiral Crowe denied any knowledge:[70] An analysis of the events by the International Strategic Studies Association described the deployment of an Aegis cruiser in the zone as irresponsible and felt that the value placed on Aegis cruisers by the US Navy had played a major part in the setting of a low threshold for opening fire.

[71] Vincennes had been nicknamed "RoboCruiser" by crew members and other US Navy ships, in reference to both its Aegis system and the supposed aggressive tendencies of its captain.

[73] Three years after the incident, Admiral Crowe admitted on American television show Nightline that Vincennes was inside Iranian territorial waters when it launched the missiles,[29] contradicting earlier Navy statements.

In speculating on the "climate" that led up to the incident, Carlson stated that the crew of Vincennes "felt a need to prove the viability of Aegis in the Persian Gulf, and that they hankered for the opportunity to show their stuff.

[64]: 5–7  George H. W. Bush, then-vice-president of the United States in the Reagan administration, defended his country at the UN by arguing that the U.S. attack had been a wartime incident and the crew of Vincennes had acted appropriately to the situation.

[89] Following the debate, Security Council Resolution 616 was passed expressing "deep distress" over the U.S. attack and "profound regret" for the loss of human lives, and stressing the need to end the Iran–Iraq War as resolved in 1987.

[97][98] Bush used the phrase frequently[99] during the 1988 presidential election campaign and promised to "never apologize for the United States" months prior to the July 1988 shoot-down[100] and as early as January 1988.

[109] In July 2014, when Malaysia Airlines Flight 17 was shot down in Ukraine, some commentators noted the discrepancy between the U.S. official position and media coverage of the two similar incidents.

The air warfare coordinator on duty received the Navy Commendation Medal, but The Washington Post reported in 1990 that the awards were for his entire tour from 1984 to 1988 and not for his actions relating to the surface engagement with Iranian gunboats.