Why is the application title bar hidden under Unity's top title bar?
Solution 1:
This looks like a subtle bug to me which seem to occur randomly in my case. To work around it, resizing the window from its bottom edge fixes the issue.
Place your cursor at the bottom of the application window in order to change it to re-size mode; and then just drag your mouse to the bottom edge of the screen. That would make the title bar visible once again.
The screenshot is when using Ubuntu GNOME, but this is how the cursor would also look in case of Unity.