Ben Goldacre, psychiatrist, occasional fMRIer and critic of rubbish medical research over at BadScience.net, has produced a radio documentary that covers many of the pitfalls of modern medical science:
Science: From Cradle to Grave
It's aimed at a general audience but there are important reminders for us in fMRI-land.
Epidemiology is a lot like fMRI when it comes to discriminating correlation from causation. As with many areas of research using human subjects, there are usually limits to the factors that can be controlled between groups, or even across time for an individual subject.
But there are often some simple things that we can measure - like heart and respiration rates during fMRI - and thus control for. Surely we should be measuring (and ideally controlling for) as many parameters as we can get our hands on, especially when the time and expense are comparatively minor. Get as much data as you can!