This is not exactly a Docker.app issue per-se, but I think it is possible to work around this: after clicking Check for Updates... and if it happens to open on top of a full screen app, if you switch spaces, you are unable to toggle via cmd+tab to that dialog. This means you have to cycle between spaces to find the dialog again as the Check for Updates... label is greyed out.
Ideally, clicking on it again would switch focus to the updates dialog.