My guess from the details provided is that you don't need to apply any patches since Apple has patched bash as part of 10.9.5. If you really aren't on 10.9.5 yet, then keep reading...
Here is what an Apple-patched as of October 8, 2014 Mac should show from terminal:
mac:~ mike$ sw_vers
ProductName: Mac OS X
mac:~ mike$ which bash && `which bash` --version
GNU bash, version 3.2.53(1)-release (x86_64-apple-darwin13)
Copyright (C) 2007 Free Software Foundation, Inc.
(If you are new to terminal, just type the parts after ** mac:~ mike$** so:
which bash && `which bash` --version
After you've compared your values, you can quit the terminal app.
If your versions are not as above, I would delete your update files and start over. Download a new patch from http://support.apple.com/kb/DL1760 and then open the console app. Look on the left for a toggle button "show log list / hide log list" and show the list. Open the triangle under /var/log and click on install.log - set a marker and then run the installer package.
Watch that log for any errors relating to the manual patch.