I think I remember seeing this come up before (maybe even I posted it?), but I couldn’t find any posts regarding it. When using Edit Scrivenings, if you go into Full Screen mode, upon exiting, the E.S. session will be dismissed. When using one of the collection modes as opposed to the selection modes, the Binder selection will be altered from the initial container to the container and all of its children. I thought at first that is what was causing the session to be dismissed, but it also dismisses when using selection mode. Not a big thing, but it would be nice if it stayed the way you have been editing it all along.
This is the sort of bug I like - ones that I have already fixed. 
Yes, I came across this bug last week when I was looking into something else. The bug is actually worse than you describe (though still minor) - if you try to click in the text of the editor after exiting a full screen E.S. session, nothing will happen for the first couple of clicks if the FS selection was towards the bottom. Basically, FS quits, then Scrivener tries to set the selection in the editor to the FS E.S. selection, fails, and then still tries to force the same selection - which may be past the bounds given that the E.S. text will be longer than a single document. This behaviour is fixed for beta 4.
Thanks,
Keith