First, I suggest you read this:
https://rainbox-dev.github.io/DuAEF_Dui ... i-use-duik
This issue is not related to Duik, it's just how the puppet tool and other effects work on shape layers.
You can not move a shape layer if you have added a puppet effect on it, as the mesh of the puppet tool do not move with the layer (spatial effects do not move with shape layers), and the part of the layer which is "cut" is the part which gets outside of the mesh.
If you just want to move it a little, you can extend the mesh a few pixels so that the part outside of the mesh are still inside it when you move the layer.