Reference Attached to Wrong Cell

The position of the reference is outside the cell record it is attached to - listed as a child of the cell record.

To fix the problem open the mentioned plugin in xEdit.

Unfold the plugin in the left tree view. Right click [+] Worldspaces. Select Apply Script...

Select the script "Put worldspace references in the right cells" and click OK to execute it.

The messages log should list the references being moved.

Close xEdit and save the plugin.

If there are issues in the area, with references or their LOD themselves, consider generating a new LOD patch from scratch.