I imagine a lot of it is that Hollywood -- here the Producers more than anyone else, possibly the writers as well -- don't understand what an NCO is. And because they don't understand, they presume that the populace won't understand.
"He leads his unit, and gives orders? But, officers lead and give orders."
"OK, ok. Let's say he's this Master Sergeant thing. We want to make his second a pilot. ... What do you mean only officers are pilots, and even a lowly Lieutenant can order him around?"
"We hear this Flint guy's popular too. Let's set him up in the sequel. Warrant Officer? What the heck's that? Waitaminute. It's also under the Lieutenant, but over the highest Sergeant?"
"Look, let's just simplify this. He's the hero of the flick, he's in charge of his squad before joining GI Joe. We'll make him an officer. People can understand officers in the lead."
Heck, look at the A-Team, that had three officers (Col, Capt, Lt.) and one enlisted (Sgt) and they got on fine.

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