- Broken Base:
- The whole "no politics" thing. While some fans appreciate the apolitical aspect of the show, many are quick to point out that neither economics or social issues are immune to skeptical inquiry (most probably it's to avoid stirring controversy).
- Related to the above is Penn and Teller's position of number one in the "Top 10 Best Pro-Science Celebrities" episode. Although no one doubts that P&T are steadfast supporters of science, they are quite controversial among skeptics for their libertarianism (in the US sense).
- Despite its ban on politics, Dunning's rather off-handed comment towards the Occupy movement in "Listener Feedback: Conspiracies" was seen as completely unnecessary by more left-wing listeners.
- Critical Research Failure:
- The DDT episode, which was heavily criticized by the Skeptical community.
- Harsherin Hindsight:
- The "Internet Paranoia" episode is much harder to listen to after Brian plead guilty for wire fraud. Especially as he explains the same type of virus (Cooking Stuffing) he was caught using
- For that matter, listening to any of the endings where Brian asks for monetary support becomes this. Many fans who gave him money saw this as a massive betrayal of trust.