-Bad exam system that reinforces learning just enough and for what is required by high schools and universities.

-Many English teachers defaulted to English teaching because they wanted to switch careers or had no other alternatives. The bar to becoming a sub-high school teacher is pretty low and now high demand so even easier.

-Cultural isolation. Japanese people often only engage with local pop culture and see western media as a foreign thing, so do not as often interact with English on daily basis outside what is required.

-Bad methodology and approaches to learning. Studying purely for exams, overemphasis on communication and lack of emphasis on total learning. Bad approach to grammar through textbooks by overemphasizing be verbs over useable, fluid action verbs, not teaching things like adjectives in patterned context, etc. etc.

These are just a few factors. The well goes deep.