When Stewie is going over the flight controls, he says that a button with a cow on it controls weapons. However, he is later seen firing with a normal control yoke.
When showing Lee Harvey Oswald waving to JFK and then later attempting to shoot at the "assassin" on the Grassy Knoll, Oswald is shown directing all of his actions to his left. In reality, both JFK and the Grassy Knoll were on Oswald's right from his window spot in the School Book Depository.
Peter is a Roman Catholic, and as such would not be permitted to have a vasectomy. (However, the show characterizes him as at best ignorant of his religion, so it's entirely possible that he doesn't care about Church dogma).
Stewi's F-117 have weapons bays drawn beneath the wings instead of the fuselage which makes no sense since there is no room.
The entire time-line makes no sense. The gap between Bertram's conception and his feud with Stewie is completely glossed over.