During the spring 2003 invasion of Iraq by U.S. and allied forces, U.S. Army Patriot air-defense missile batteries were so dangerously unreliable—and prone to firing on friendly planes—that they provoked a brief, and today largely forgotten, civil war between missileers and fighter pilots.

“Many allied pilots believed that the Patriot posed a greater threat to them than did any [surface-to-air missile] in Iraq’s inventory,” Benjamin Lambeth wrote in his exhaustive Iraq war monograph The Unseen War.

“The Patriots scared the Hell out of us,” one F-16 pilot remarked. As Army missiles downed two allied warplanes, killing three crewmen, fliers did their best to avoid the trigger-happy Patriot batteries—and in one case an Air Force pilot actually fired on a Patriot crew.

When American and coalition armored battalions swept into Iraq in March 2003, 62 Patriot firing units followed behind them, maintaining a continuous air-defense screen just behind the front lines.

America’s main ground-based air-defense system, Patriot combines a radar, a control trailer and—for early versions—several quad-pack missile launchers, all mounted on heavy trucks. A Patriot can shoot down aircraft up to a hundred miles away. Some versions can intercept incoming ballistic missiles, although critics have questioned the Patriot’s effectiveness in this role.

In 2003, there were serious deficiencies in the Patriot’s software. The system applies complex computer algorithms to judge a target’s speed and altitude and, in the case of an airplane, its radio transponder signal. If the computer decides a bogey matches the profile of an enemy aircraft or missile, it displays the target as hostile on operators’ screens.

In certain modes, the Patriot can even automatically launch a missile at a radar return it decides is a bad guy.

The Patriot’s computer and human minders don’t always get it right. On March 23, a Patriot battery shot down a Royal Air Force Tornado fighter-bomber returning to Kuwait after a mission over Iraq. The two crew died.

“Early speculation attributed the incident to either a failure of the Tornado crew to identify their aircraft properly to allied acquisition and tracking radar controllers or a failure of the Patriot battery operators to interpret correctly the Tornado’s IFF signal,” Lambeth wrote.

IFF is Identification Friend or Foe—a radio signal that warplanes emit to identify themselves. The latest planes have multiple IFF systems, including encrypted and non-encrypted versions.

According to Lambeth, the British ultimately blamed the fratricide on the Tornado’s malfunctioning IFF, but one “unofficial account” claimed the Patriot system misidentified the Tornado as an Iraqi missile.

In any event, the Patriots quickly proved an awful menace. “Allied aircrews experienced a notable spike in their stress levels whenever they operated within a Patriot threat envelope,” Lambeth reported. “More than a few who were locked up by a Patriot radar had been forced to drop chaff, engage in aggressive countermaneuvering and make frantic calls to the AWACS [radar control planes] to get the offending Patriot to break its lock.”

U.S. Air Force pilots quickly lost patience with the Army missileers. One day after the Tornado shoot-down, an F-16 pilot was flying over An Najaf in Iraq when a Patriot radar zeroed in on him. The flier fired a HARM anti-radar missile that destroyed the Patriot’s sensor dish but, luckily, did not harm the Army crew.

The Air Force insisted the F-16’s attack was accidental—that the pilot did not know that the radar he was shooting at was a Patriot manned by fellow Americans.

But other airmen were unapologetic. “Those guys were locking us up on a regular basis,” one F-16 pilot said. “No one was hurt when the Patriot was hit, thank God, but from our perspective they’re now down one radar. That’s one radar they can’t target us with any more.”

But there were still dozens of Patriots in the war zone. And on April 2, a Patriot shot down a U.S. Navy F/A-18 fighter over southern Iraq, killing the pilot. The F/A-18 pilot had detected the incoming missile and had tried to dodge it. His wingman survived the engagement. The Navy, Lambeth wrote, was “understandably distressed.”

Again, the murderous Patriot had apparently decided the Navy plane was an Iraqi rocket.

U.S. commanders ordered safety measures. They barred Patriot crews from placing their missile launchers on fully automatic modes. They told pilots to use the more-reliable non-encrypted IFF. The Army promised it would fix the Patriots.

Studying the Patriots-versus-friendly jets conflict after the invasion, the U.S. Defense Science Board expressed deep worry. After all, Iraq had offered only token resistance to the allied air campaign. Iraqi jets never counter-attacked. Baghdad launched only a few ballistic missiles.

Future wars “will likely be more stressing,” the DSB warned. If the Patriot batteries couldn’t cope with an essentially one-sided aerial battle without accidentally killing three allied airmen, how would the missileers fare against a sophisticated and determined foe?

David Axe serves as Defense Editor of the National Interest. He is the author of the graphic novels  War Fix, War Is Boring and Machete Squad.