Revealing mistake: Gruesome but wrong. When the other pilot is murdered, the killer shoots him in the neck pointing downwards, but the spray of the blood-pack is from his forehead up high. (00:31:20)

Revealing mistake: When Stackhouse is shot, the smoke doesn't come from the gun. It comes from the hill. (00:31:30)
Revealing mistake: When Chris Burnett runs out in front of the pickup truck to get a ride, the pickup skids to a stop - you can see a person sitting in the bed of the truck and he does not get even slightly startled by the truck's sudden stopping. (01:02:55)
Revealing mistake: When the tank bursts into the building it fires and Burnett flies through the air landing on a table. It is a stunt double, cause his hair is shorter and darker. (01:09:45)
Revealing mistake: When Owen Wilson is trying to restart the beacon in his ejection seat, his right hand is ungloved. Yet in the scene before, he took off his left glove. It is my belief the negative is reversed, as you can catch a quick view of a Duracell battery with the letters mirrored. (01:24:43)

Revealing mistake: When Burnett stabs Sasha the sniper with the flare, you can see the outline of the padding visible under his blue jacket. (01:29:20)
Revealing mistake: Towards the end of the movie when Burnett is by the plane's ejection seat, you see a puddle of water by him with snow flakes floating on top of the water. Snow flakes dissolve in water as soon as they hit. They use a corn starch type mixture to make fake snow, and that is what you are seeing in this scene.
Answer: The two seats collided in midair before their chutes opened and Stackhouse yelled, "ow!" Not realistic because in the 5 seconds it took for the second pilot to eject they would have been far apart.
But you see his leg get injured before his leaves the jet. I think the original question refers to how did that happen.
Ssiscool ★
The injury to Stackhouse's leg was from a pen attached to his knee pad. When watched in slow motion, you see it disintegrate and somehow throw shrapnel into his leg. It makes little sense, I believe it was merely a plot point to make Stackhouse unable to travel out of harm's way. This prompted Burnett to leave him unattended for the bad guys to find him as he went to higher ground to get better reception on the PRC-90.