Every time a new feature is introduced, the binary format likely gets changed.
http://esotericsoftware.com/support#What-version-of-Spine-works-with-what-version-of-the-Spine-Runtimes
Like any software dependency, updating the Spine Runtimes should be done with caution. For example, right before your application release is not a good time. Typically animators should use a specific Spine version so that the Spine version and Spine Runtimes version stays in sync.
This means whenever you update your Spine editor, you need to update your Spine runtimes.
And whenever you update your Spine runtimes, you need to export your files again.
Between minor updates it is likely okay, but big jumps like between 3.0 and 3.1, and 3.1 to 3.2, and 3.3 coming soon, include significant changes.
If you are using Unity, you can update your runtime to spine-csharp 3.2 beta with this unitypackage: http://esotericsoftware.com/files/runtimes/unity/spine-csharp-3_2_beta2.unitypackage
But with that update, if you are using binary, you will still need to re-export your skeletons.
[EDIT] The link and file has been updated. The previous beta had a problem.
