The technically are "stacked". Can you perhaps attach an image or the like for me to have a better view of the issue?
I'm not sure what the issue is. It most likely is something about the grid; when I look at the files on my end, they overlap as they should. I've never had this issue come up before.
Some things that could be the issue:
- Sorting for isometric/2D is off
- Different import settings between the two sprites If PPU/pivot/mesh type differ
- Grid / cell size mismatch (the grid should be true isometric, not 1:2)