paatz04 It's just a guess, but are you perhaps updating an existing skeleton asset set and are having leftover atlas assets like textures in your project? If so, are you perhaps only partially overwriting the texture assets with the new ones without deleting the old set? In general it's always recommended to delete that old atlas textures (just the old .png texture files, not the atlas.txt file and not the .meta files) before copying the new atlas assets into the same directory.
Rather unlikley: are you perhaps using a special folder structure where the atlas files end up separate from the skeleton, and are perhaps using the wrong atlas set from another directory?
If that does not resolve the issue, as Mario mentioned, we would need a small Unity project which reproduces the issue in order to help better. If it's hard to reproduce, please copy the project as soon as it occurs and then try to remove all unneed assets. You could send us a zip file of your project to contact@esotericsoftware.com, briefly mentioning this forum thread URL for context, then we can have a look at it.
