One of the aircraft performing flight displays at the Farnborough Airshow in England this month is the Yakovlev Yak-130 advanced trainer, shown below (image courtesy of Wikipedia).
Yakovlev vice-president Konstantin Popovich said that on the first day of the show, air traffic control initially refused to allow the Yak-130 to take off, because its air intakes were closed. ATC thought this indicated a problem with the aircraft.
As you can see from the photograph above, in the case of the Yak-130, "that's not a bug - that's a feature!". It's designed to operate from poor-quality airfields if necessary, so the air intakes (circled in red) are masked by retractable covers during taxiing and take-off, to avoid ingesting debris into the twin jet engines. They draw air instead from a series of vents that open above the air intakes (also visible in the red circle in the photograph above). When the jet is safely off the ground, the 'normal' air intakes open and the upper ones close, restoring the aircraft's appearance to something less puzzling to uninformed observers.
It certainly looks odd, doesn't it? One can hardly blame the poor air traffic controller for thinking something was wrong . . .
EDITED TO ADD: I found this video of the Yak-130's flying demonstration at Farnborough two days ago. Enjoy!