& Continuous Learning

I saw a really great post on the Freakonomics blog talking about how hidden connections almost sunk Chicago.  I've seen situations like this all too often during my career.  At least in the software world, we can try to prevent this by developing modules that are more loosely coupled.  Of course, in the real world you are often inheriting years upon years of past decisions made by anonymous developers.  In the absence of a thorough end-to-end testing suite, is there anything you can do to prevent this?