Maybe It's because of El Capitan (Trust me I'm a mac user too) maybe FFMPEG or Homebrew doesn't support El Capitan yet (Probably FFMPEG).
That's what I'm starting to think to be honest, because I don't know what's going on.
I followed this tutorial and was running ffmpeg and could do all the different ffmpeg commands in Terminal, but then after a few minutes I go back to Terminal and it stops working, acting if the command doesn't exist.