Factual error: When Blackthorne is on Rodrigues' ship, Rodrigues offers him grog. But grog was only invented in 1740, by British Vice Admiral Edward Vernon, whose nickname was "Old Grog" because of his preference for coats made of grogram cloth.
Factual error: At the end when Skeksis enters the crystal chamber, in the overhead shot you can see 22 arcane symbols around the crystal when there should only be 18, one for each exiled skeksis. (00:45:53)