Luckily yes, that black square/vertical rectangle only appears at the very end. Moreover, the most amusing and absurd thing is that if you hold down the left mouse button, then this black line will begin to grow faster until it turns into this vertical rectangle, which will completely obscure Mya.
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.