Weird, I fixed that bug sometimes ago.
But you can press Select at the start of the cutscene (0.5s window to do that) to skip it and still get the Good Ending.
I have made a patch on this page, you can check it out.
But if the bug still occurs, you can load the previous save, press Select button at the start of the cutscene (that's how I do when debugging) to skip it (you can skip most of the cutscenes in this game with Select). After that you get the Good Ending.