Did that black square only appear in the last scene...? Definitely a glitch with the video player, but I haven't encountered that. I'm afraid I don't know what could be causing it D:
In the two endings I've gotten to, after Mya says her last words, a black line appears at the bottom and grows upward until it becomes a vertical rectangle. And no, restarting the game didn't help. But since this black rectangle appears only at the end of the game, it does not really spoil the mood. In other words, this bug is not critical, you(or I(?)) can play.