Pilots have been seeing unexplained things outside their cockpit windows since the dawn of aviation.
One of the most legendary examples happened near the end of World War II when both Allied and German pilots reported seeing fiery glowing objects that followed their planes and then disappeared in wild maneuvers.
The sky phantoms were nicknamed foo-fighters (long before the 1990s alternative rock band), and thought to be secret military weapons. The term "UFO" didn't appear until a few years later - at the height of anticipation over the eventuality of human space travel.
"... the number of fatalities in airline accidents caused by UFOs equals the number of motorists killed in vehicle collisions with unicorns."
In the Oct. 19th, an issue of U.S. News & World Report, editor Michael Morella warns that UFOs distract pilots and can cause air disasters.
To the best of my knowledge there has never been a documented commercial air crash attributed to a cockpit distraction due to a UFO buzzing outside. Historically, pilot distractions inside the cockpit have triggered crashes, including: pilot chitchat, misreading of instruments, preoccupation with certain flight controls, and other loss of situational awareness. There isn't one flight recorder transcript I know of where, in the doomed flight's final minutes, the pilot says: "Is that an alien spaceship out there?"
UFO debunker Robert Sheaffer puts it more bluntly blog: "... the number of fatalities in airline accidents caused by UFOs equals the number of motorists killed in vehicle collisions with unicorns."
There is a legendary case of a military aircraft crashing during a UFO pursuit. In January 1948, four P-51 Mustang fighters were rerouted to check out an object described as one fourth the angular size of the full moon (the diameter was estimated to be 300 feet, but this can't be calculated without knowing the object's distance). The P-51s broke off the pursuit except for one pilot Thomas Mantell who climbed to 25,000 feet without oxygen, blacked out, and spiraled to a crash landing.
As is symptomatic of UFO hyperbole, this story has been embellished with claims the UFO was gigantic and metallic, and it perhaps used a space weapon on Mantell to keep him away. The incident was a game-changer for belief in UFOs at the time. UFOs could shoot back! The simplest explanation is that Mantell was chasing a silver 30-foot diameter secret Navy high altitude balloon. (Another secret balloon probably crashed in Roswell, New Mexico in the summer of 1947, but that's another story.)
Yes, there are decades of pilots reporting oddball lights in the sky spooking them, and even a New York Times best-seller entitled: "UFOs: Generals, Pilots, and Government Officials Go on the Record." But there has never been a corroborated report of a truly exotic vehicle of obvious extraterrestrial construction (something more than a blob, a Frisbee-looking thing, or other primitive geometric shape) ever being seen in broad daylight and up close.
This is ironic when considering the oddball case of the lawn chair UFO. On July 2nd, 1982, truck driver Larry Walters tied 42 helium-filled balloons to a lawn chair in the backyard of his girlfriend's house in San Pedro, Calif. He shot up to 16,000 feet where a TWA pilot incredulously reported the details of seeing a man adrift like the character in the 2009 cartoon "Up."
An interstellar spaceship zooming through the clouds should make a much bigger impression on pilots. But this has never happened despite thousands of UFO reports per year.
UFOs are almost exclusively seen as just weird lights. And, often the misinterpretation is made that the lights are attached to a physical body, as in the case of the legendary Phoenix lights sighting in 1997 (which Morella references as an outstanding UFO mystery). The Phoenix lights have been debunked as a hoax where flares were attached to a series of helium balloons. Witnesses' imaginations filled in the nonexistent details to describe a monstrous flying delta-shaped vehicle.
Similarly, a report from 1968 describes a cigar shaped object with rectangular windows (a commercial alien tourist spaceliner?), when it was really found to be the breakup of a a Soviet satellite, as tracked by NORAD.