I get this when Undoing after calling Undo.RegisterCompleteObjectUndo(transform, "Foo"); (no stack trace).
Warning is printed regardless of whether the transform has a parent or not. Scale is 1,1,1.
Interestingly, the warning is printed twice. However, if I used Undo.RecordObject instead, it is printed only once.
This can probably safely be ignored until it is fixed.