Native English speakers never have difficulty learning which prepositions to use. On the other hand I often hear even quite fluent second-languagers stumble over things like “Independent from, er… independent of.” (As in, X is independent of Y.) Is this just because children are better at learning language than adults? That probably explains a lot. But as I have speculated before I think there are some aspects of the difference between adults and children that don’t require an appeal to brain differences.
Adults are building on stuff they already know, children are learning for the first time. Adults know what a preposition is and that “from” and “of” are both prepositions. They know grammar and they think in terms of grammatical structure. So they search through the prepositions they know that would play the right grammatical role.
Children don’t think about language, they just copy what they hear. They don’t hear “independent from” so they never consider saying that. Of course adults learning English don’t hear “independent from” either. The fact that they still make the mistake means that they don’t learn purely by imitation like children. They make use of the rules they already know.