As Sheldon describes the first episode of Star Trek: The Next Generation (1987), he makes it seem as though Wil Wheaton's Wesley Crusher appears right away. Wil didn't make his first appearance until around the 33.5 min mark.
Sheldon states that Wil Wheaton is the only person he knows that has been immortalized in 1/16 scale. This is not true because he also knows Brent Spiner, who was also on Star Trek: The Next Generation (1987) and his character was also made into an action figure.
During "Fun With Flags" scenes, filter effects are applied to simulate viewing the action through the lens of Sheldon's digital video camera. This makes the image appear desaturated and slightly pixelated. That pixelated filter has been left on by mistake later in this episode in some shots as Leonard and Sheldon call up Amy. Specifically, the shots filmed through the rightmost camera of the stage.
During the opening filming of 'Fun with Flags', the camera that Sheldon and Wil are addressing is several yards to Amy's left, rather than the one she is supposed to be filming with.
Throughout the episode, Amy complains that Wil was rude to her, when in fact all he said was that Amy was being a "pain in the ass". Amy was far ruder to Wil than he was to her and she should have apologized to him.