The recommended way is always to "strip whitespace"/"trim whitespace" BEFORE importing into Spine.
If you use Meshes, Meshes require that you never change the whitespace because it uses unstripped coordinates and can't reliably use anything else.
So if you export or pack the atlas from Spine and use whitespace stripping and whitespace changes/gets removed, this will happen.
This is not a bug, it's a technical and common limitation. If there's a bug, it's that there isn't a warning for users. (But I can understand that there are ways of implementing it where it can slow down if Spine has to check. @Nate, @Shiu, if this can't be done, maybe it should just be off by default and the whitespace stripping checkboxes should be categorized under an advanced heading and labeled with a scary WARNING symbol? I would do that either way.)
Anyway...
I don't know what to recommend as an easy fix.
You will likely need to do some work again. You need to re-export your character's individual body parts from Photoshop (or your drawing program) already whitespace-stripped and import them into Spine again. If you did any mesh animations, they will likely be deleted in the process.
If you need help doing this, let us know what tools you are using.