One of the better examples that I have found of this distinction is with physical activity. Travis Saunders talks about the difference between a closely monitored exercise program and encouraging exercise related behavior (despite randomization).
This should be a warning for those of us in drug research as well; not even randomization will help if you have a lot of cross-overs over time or if user tend to alter other behaviors as a result of therapy. This isn't very plausible with some drugs with few side effects (statins) but could be really important for others where the effects can alter behavior (NSAIDs). In particular, it makes me wonder about our actual ability to use randomized experiments of pain medication for arthritis (except, possibly, in the context of comparative effectiveness).
But it is worth thinking about when trying to interpret observational data. What else could you be missing?