The font (which includes all symbols incorporated therein) is encoded in 2BPP, which for the sake of this discussion means that only four colors, including "invisible," are possible. The game uses all three colors: color #1 is the primary font color, white in most situations; color #2 is the color of the window, blue by default, the negative space for all font characters; color #3 is (usually) gray, used as an accent color in weapon, magic, etc. symbols. So black is not an option, hence "invisible" is used where black is needed. In most cases it appears as black because it's in front of a black background, but when it appears in battle or in dialogue, it takes on the color of whatever is behind the text box. "Fixing" this would be a considerable undertaking, or maybe even impossible given the way the SNES PPU works.