Steps to reproduce:
1. Download and open attached project "New Unity Project 11.zip" (Or have a project with a lot of scenes, e.g. one hundred, in project tab)
2. Open all of the scenes, so they are in Hierarchy window
3. Delete the scenes from Project tab
4. Delete all the scenes in Hierarchy

Actual result: Deletion confirmation dialog that does not fit in screen (https://gyazo.com/fb87862e387c5cc281cc53321486fd99)
Expected result: Item list is collapsed (e.g. https://gyazo.com/2606db632a18c5634f66419964a150ed)

Workaround: Clicking on dialog window to bring it to focus and pressing enter (or escape button) resolves it.

Tested and reproduced on:
Window 10
Unity 5.3.3f1, 5.4.0b8
Could not reproduce prior 5.3 due to multiscene editing