Deliberate mistake: The French NATO rescue team is flying an old, Russian-made Mi-17 helicopter which is not in service in France. It was probably rented in Slovakia where most of the film was shot. The Mi-17 is easily distinguished from the French multi-purpose helicopter Puma: the Mi-17's landing gear is supported by huge rods, its side windows are round, and it has a sleek boom with the tail rotor on the left side. The Puma has smaller gear support, rectangular side windows, and a thicker boom with the tail rotor on the right side. (01:15:42)
Deliberate mistake: The aft cockpit of the F/A-18F is not simply a 'Navigator' as they say several times in the movie. It is the Weapons Systems Operator, or WSO (Wizzo).
Answer: It is possible that he has done of one two things. Banged his leg on something inside the cockpit causing it to break, or landed too hard on his way down. It is common for people to break limbs when parachuting/sky diving. It is possible that his bones were just not up to withstanding the force which he incurred.
Scrappy
Or a piece of shrapnel from the jet breaking apart cut his leg.