Are you talking about the black bars on the sides of the screen when you're playing in full-screen? If so, that's due to this game's native 4:3 aspect ratio that tries to give the game a more authentic retro-game vibe, so the black bars are completely normal.
Without the black bars, some sort of stretching would occur and it would mess with the pixel-art quite a bit. Please do let me know if the black bars are not the issue with full-screen mode.