Repro:
1. Create a new 3D project
2. Add the Shadergraph package to it, create a new PBR graph and open it
3. Uninstall the Shadergraph package
4. Observe the still open Shadergraph Window

Expected result: the leftover container window can be closed (using title bar buttons) or be closed automatically if not alone in the dock area.
Actual result: the leftover Window has no close button and cannot be moved out of the way. Reinstalling the package again does not fix the issue and it can only be fixed by resetting the Layout

Reproduces in VFX, as well as any custom editor window script.
Repro for custom window script:
1) Create a custom window script; take something form here: https://docs.unity3d.com/Manual/editor-EditorWindows.html
2) Open it via the custom menu system
3) While it's still open, delete the underlying script

Or by closing it through the menu (see video).

Reproduced in:
2019.2.0a12 (With Shadergraph versions: 6.5.3; 5.2.3)
Shader Graph in SRP master of 4/18/19
VFX preview-6.6.1