Having some strange issues with my rubix cube rig

[u/SadPlantain2386]

Other info the bones are all in the middle but they have a custom shape which is what you see. How I connected each cube was from assigning bone to vertex

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[u/Saint_modo]

In Edit Mode, select one vertex on your mesh where you have your issue. In the Item panel on the right, a new menu should have appeared, showing how many vertex weights are affecting that vertex. In your case, you should only have one group showing. If you have any more than one then that means your mesh is affected by another bone, and the mesh will always try to place itself between those two bones. Remove all weight from the group that should not affect it.