On Aseprite v1.2.13 x64, when you use the “new sprite from selection” option from an indexed color file that uses a transparent color (as set in the advanced section of “Sprite Properties”), the new sprite’s transparent color is automatically set to an index different than the original: It is always set to 1 index over the sprites’ actual number of colors, which is an invalid value.
For instance, say I have a sprite with a 6-color palette that uses color index 0 for its transparency, selecting a part of that image and clicking “new sprite from selection” creates a new sprite, which has color index 6 set as its transparent color. The sprite’s last color index being color 5, it means the image just has no transparency at all.