Hello,
Could it be that you are exporting a gif or video and not using the runtimes? If you are exporting something with a blending mode applied to it against a transparent background to gif/video/png formats, the results may not be as expected.
If instead it's the atlas that is not outputting all of the meshes, or none at all, then we'd need to have a better look. For example, if you can't share the project, we need to at least know the Spine version you are using, the export settings you used, and see the incorrect result. (or at least a portion like in your screenshot above)
