Hi, I had same issue. 
Is your node, rotation of which you wanna to change is KinematicBody?
So, I need to tell u, that you can't simply change KinematicBody's transform anyhow.
It's need to change by move_and_slide or something like this...
If you really want to set rotation or something else in transform,
then I advice you put your KinematicBody in some node... for example Node2D
This allow you to change rotation of Node2D and KinematicBody accordingly.
Hope it's save you a day. Good luck