White Square in the menu bar (Not a hardware issue)

Hi there,
I have a Macbook Pro 13" with Retina display (late 2012), and I recently updated Mac OS to Yosemite.
After updating, I have noticed that there is a white square in my menu bar and I do not know how to fix it, I can tell that it isn't a dead pixel as I can zoom into it and it will not remain in the same place, it will zoom in normally as if it is 'stuck' on the screen, I will add some screenshots to explain my issue:
As you can see here, there is a white square in the menu bar near the centre of the screen at the top.
When I zoom in, it moves to suit, and if I place my cursor over the white square, then it disappears as if it is a layer below the cursor, below shows how it doesn't stay in the top of the screen when I zoom in:

Maybe NSPopover (Safari's 'Show downloads' uses one, for example)?

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