I don't use RPG maker. The issue is that individual sprites are NOT multiples of 16. My suggestion is not resizing them to make them multiples of 16, but PADDING to make the width/height multiples of 16.
Ah, so it is not alignment issue, but rather because of cell size I see... If that's the issue I'll consider it for the next updates.
My suggestion for animated sprites is by not relying them to the certain tilesets size, but by height-weight division (row x height = 3 x 4), therefore you don't have to rely on fixed tilesizes (e.g must be multiplication of 16, 24, or 32, etc) when you get your assets from different people with different standards.