Colors incorrect?

[evanmalmud]

With the export by tag script it seems like sometimes the colors are messed up.
Will upload an example of the export by aeseprite in a single file VS the export by tag of the exact same file.
google drive link

If you compare the top animation of the sprite sheet to the Ind-Idle.png you can see the color of the shirt changes.

There are other issues as well I've noticed in sprite ordering sometimes as well.