Since the latest update the background eraser tool is bugged, after clicking just once the function doesn't stops and keeps erasing things until you hit ESC. My Photoshop version: 2015.0529.r.88x64 (OSX 10.11.4)
Maybe you need to trash your Prefs? I have no problem whatsoever with the Background Eraser, no matter what I set it to. But I'm on Yosemite, not El Capitan, because there seem to have been a lot of problems associated with El Capitan. However, sometimes with updates Preferences do need to be deleted and a fresh set created.
If that doesn't do the trick, maybe giving us the specific settings you're using will help.