Pharan wroteWhat you're running into seems to be this: Premultiply Alpha
Photoshop is unforunately not good for editing the atlas if it was packed with premultiply alpha. Photoshop does not support preserving PMA; it will apply bleed without asking the user.
If you want to be able to edit the atlas in Photoshop, you have to choose a straight alpha workflow. That means disabling premultiply alpha in texture packer, and choosing a non-PMA shader like
Sprites/Default
.
Thank you a lot, this clarified a lot the things for me!
If someone had the same problem, Krita doesn't seem to have this problem.