Black squares sounds like scenes that are not yet drawn. Drawn scenes have a greyed out image that will then have color after it is unlocked. Though if there is any specific scene that should be drawn not showing, please tell me the scene and I will take a look.
No, only the scenes I wrote in the first message are not seen and they are the ones with the black squares.
The others all appeared to me.
The only thing I would like to point out is that every time you restart the game, once you have completed a Route, if you decide to leave the gallery as it is without redoing everything, Gomamon will have the hearts or the dick for the entire game, unlike when you decide to delete the gallery.