In Ubuntu 14.04, The title bar of my application goes under the main title bar of Unity.
In the image below, the selected window is of Download Manager, but its title bar is hidden under unity's top title bar.
I find this issue occurring with web apps and standalone apps.
Ideally it should look like this:
Best Answer
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.