When it comes to high level logic and critical thinking courses than I would propose a course that centers on fundamental questions.

Focus real world scientific debates, where there's disagreement but how we interpret evidence:

1) From John Ioannidis:

Studies have gone back and forth on the cancer-preventing powers of vitamins A, D, and E; on the heart-health benefits of eating fat and carbs; and even on the question of whether being overweight is more likely to extend or shorten your life. How should we choose among these dueling, high-profile nutritional findings? Ioannidis suggests a simple approach: ignore them all.

2) Richard Feymann article about Cargo Cult science: http://www.lhup.edu/~DSIMANEK/cargocul.htm How much of science today suffers from that problem? (Voodoo neuroscience: http://neurocritic.blogspot.de/2009/01/voodoo-correlations-in-social.html)

3) Was the Journal of Personality and Social Psychology wrong to publish Bem et al 2011?

4) Is Nassim Taleb right when he calls for the abolition of the Nobel Prize for Economics? Does the prize do good for the world?

5) The case of NASA claiming that "The definition of life has just expanded,"

There probably a bunch of other nice edge cases that are worthy of discussion. Philosophers should analyse where other fields mess up.