I find the biggest difficulty in language learning is how toto be mastering habitual usage.

I don't think "habitual usage" is the correct term here. What exactly are you trying to say?

Many language learners can makeform sentences that are grammatically correct, but native speakers never say them that way, though they can fully understand the meaning of the sentence. However, those sentences are often ones native speakers would never use, albeit their meanings would be fully understood.

I believe thea majority of the learners would agree with my opinion.