According to yesterday’s NHK video, the JCG aircraft didn’t immediately come to a stop on the runway. Can’t post links: search for NHK new details emerge on Tokyo Haneda airport collision.

It appears that it either missed the hold position or received the instructions too late as it taxied from left to right, made a 180 turn and entered the runway and then taxied from right to left to the hold position. 40 seconds after it came to a stop the JAL aircraft slammed into it from a right to left direction.