This is purely speculation on my part but I flew for JAL for nearly 15 years. What I have witnessed during those years was that while the English proficiency level of JAL pilots are acceptable for international operations, proficiency levels of the non-civilian Japanese pilots are usually not that great. That could have led to a mis-understanding of an ATC instruction by the Coast Guard crew as most of the time (unlike China, France etc.) Japanese ATC speaks English to even the Japanese pilots. RIP to those who perished.