Soft Target - S2-E6
Character mistake: On the roof, Don and the other agents have their weapons drawn on James Grace, who is holding Houseman hostage with the fake bomb. Once Grace is taken away, the threat is gone. But Don still has his gun pointed at Houseman, with his finger on the trigger. Houseman, while Don might think is a jerk, was innocent of any crime. There's no reason an agent like Don would have his gun pointed at him.
Character mistake: In the epilogue, Charlie illustrates the relationship of mathematics to real life by discussing the golden ratio and its presence in a host of real-life situations, including the shape of a nautilus shell and the distribution of petals in a flower. These claims are disputed by some mathematicians (see http://en.wikipedia.org/wiki/Golden_ratio#Nature), and the one about the nautilus shell one is untrue (see http://en.wikipedia.org/wiki/Golden_spiral#Spirals_in_nature). It's possible Charlie is just repeating what he has read or heard without investigating it for himself, but this is uncharacteristic of him.