I can think of one possibility....
The language of international aviation is English and flight crews and air traffic controllers are presumed to be fluent in English regarding aviation terms and commands.
But... I wonder how proficient in English Japanese Coast Guard pilots are? Likewise, what language do Japanese military air traffic controllers use?
If Japanese military and coast guard aviators frequently use Japanese, the small difference between say: "Cleared to pre take off holding area" and "Cleared for take off" might have been misunderstood by the Coast Guard crew.
As a side note, language confusion led to one aviation disaster when a Spanish speaking pilot was dangerously low on fuel and being delayed by ATC. The pilot repeatedly requested a "priority landing" in English. The ATC then cut him in line a few planes. But... the pilot should have used the term "emergency landing".