"Ex Marks the Spot" sets Joan of Arc during her Orleans campaign and Johann Gutenberg as direct contemporaries. Joan of Arc was burnt at the stake in 1431; Gutenberg did not invent his printing press until 1456, almost thirty years later.
During his explanation of the decay or "unraveling" of the past, Larry states that Henry Ford's Model T was the basis for all of the future's cars. In fact, there were quite a few other relatively light powered vehicles (gasoline or otherwise), such as the Stanley Steamer, that predate (and inspired) the Model T.
While George Washington Carver did have a brother, he was older than George and died over a year before George's birth. Since their mother was kidnapped and killed during a raid on the Carver estate 5 months after George was born, he could not have had a younger brother, named Todd or otherwise.
The mission in "Father Figure of Our Country" is set in 1778, and George Washington is constantly referred to as the President. In reality, he was still fighting the British in 1778 and did not become president until 1789.
In the episode where the Time Squad meet Alfred Nobel in Sweden, Tuddrussel is greeted by a Swede who says "Guten Morgen" - which is German, not Swedish, for "good morning". In Swedish it would be "god morgon".