I think there is are slight inaccuracies with the palette of the outside tileset. As far as I know, all colors in ALTTP have RGB values that are multiples of 8. For example, in the dungeon tilesets, the blue tiles used for deep water should be 56,96,168. This is the value I have from Hyrule Magic. (Or 88, 128, 200 in the PAL version, because there is an offset of 32 for all 3 RGB values). In your tileset, this color is currently 57,99,173. Not a huge difference, but when transitioning from a map made with my old tilesets to a map made with yours, the difference is visible.
It looks like this rule is better respected in your dungeon tilesets.