This can't be a common MacBook Pro problem, or I would have found a solution more easily.
But fairly often my 13 inch Retina MacBook Pro presents me with a black OS X menu bar at the top of the screen after I've closed and opened the cover. About all I can make out is the American flag on the right side.
The black pixels that comprise the other icons are almost completely hidden, being black on black. When I'm using Safari, I have to visualize where the File menu, or whatever, is, then fiddle away in the dark to choose a menu function.
Here's the solution I've found: I maximize the Safari window using the diagonal arrow thingie in the upper right hand corner. Then I revert back to the usual window size by pressing "esc." Bingo, the bad black goes bye-bye.
Another solution offered up in this discussion thread is to click on the notifications icon on the far right side of the menu bar. But, of course, you have to be able to find the icon in the dark to do that. I like my approach better.