Is there a way I can find what file handles emacs has open, and close these references? Or even better, find where they are being open?

Emacs is keeping handles to a large number of files (a leak) that I don't have corresponding buffers to. My standard method of closing a buffer has been using the `kill-buffer` command.

## Context:
I am having a reoccurring issue, where after a day or two of being open I can no longer do any file operations in emacs, due to a "Too many open files" error when creating a pipe. I am on OSX 10.10.4, Emacs 25.0.50 installed with homebrew.

Here is a sample of emacs' open files according to Activity Monitor (double click on emacs and select "Open Files and Ports").

    /Users/Ash/Dropbox/org
    /Users/Ash/Dropbox/org
    /Users/Ash/Dropbox/org
    /Users/Ash/Dropbox/org
    /Users/Ash/Documents/workspace/roboclub/Federation-Place
    /Users/Ash/Documents/workspace/roboclub/Federation-Place
    /Users/Ash/Documents/workspace/roboclub/Federation-Place
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site/src/javascript/status
    /Users/Ash/Dropbox/org
    /Users/Ash/Dropbox/org
    /Users/Ash/Dropbox/org
    /Users/Ash/Dropbox/org
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site/src/javascript/status
    /Users/Ash/Documents/workspace/roboclub/Federation-Place
    /Users/Ash/Documents/workspace/roboclub/Federation-Place
    /Users/Ash/Documents/workspace/roboclub/Federation-Place
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site/src/javascript/status
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site/src/javascript/status
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site/src/javascript/status
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site/src/javascript/status
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site/src/javascript
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site/src/javascript
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site/src/javascript
    /Users/Ash/Documents/workspace/roboclub/Federation-Place/web/site/src/javascript

There are actually many more files open, but you can see that they are being repeated. (Also these are folders, not sure why that is).