I have been experiencing some odd issues when placing prefabs onto my 3D UIRoot. Never had that issue before, so I am not sure what could be causing it. What happens is basically that multiple UIRoots (really a lot) get added to my hierachy when dragging a prefab onto my UI Root. It looks like a new one is created each frame while my prefab is being dragged over the Scene viewport. This leads to dozends of new UIRoots which need to be deleted manually.
For me it is pretty much a 100% repro even with a clean project and scene. To reproduce try:
- With Unity 5.0.0f4 / NGUI 3.8.1, create a new project, and new scene
- NGUI -> Create -> 3D UI (Issue does not happen with 2D UI)
- On 'UI Root (3D)' create any new NGUI element (sprite, widget, label, ...)
- Drag the new element into the project view to create a new prefab from it
- Drag the new prefab back onto your UI Root
moving the mouse over the scene viewportThis issue can be worked around by making sure to not touch the viewport with the mouse while adding the prefab to the scene, however it is pretty annoying

Not sure if this a known issue or something is wrong with my project setup but I am pretty sure I did not experience this in earlier NGUI versions.