I've run into this small problem umpteen times, and it happens most often on my 13 inch MacBook Pro Retina, and usually after disconnecting from my external displays and running off the built-in screen alone.
I begin work on a new document (most often in MS Word) but it happens in other applications too. When I go to save, and the Save/Save As dialogue box appears, I'm able to navigate to the correct location, but then (being the *cough* organised person that I occasionally am) I often want to create a new subfolder, only to find that the New Folder button is missing - off the screen and at least partially concealed behind or beyond the Dock. This usually means having to save it in a temporary location that I CAN reach and then jumping into Finder, creating the new folder and moving the file etc, etc. Both tedious and annoying.
Here's a tip to get around the issue without leaving the Save As dialogue box:
The Save/Save As dialogue box has two modes. A full, 'Finder-like', Expanded mode view showing the locations of all your favourites and additional options, and then a Collapsed mode view which is more abbreviated and lacks access to your Finder Favourites etc. The trick to getting around the problem is simply to toggle between the two modes.
Click the disclosure triangle to the right of the Save As filename box and you'll toggle from Expanded to Collapsed view, click it again and the Expanded view will return, but this time reformatted to fit your screen a little better, AND (importantly) with the New Folder button visible! It's still a little clunky, but it gets you out of trouble.