After Jane hides under the rug (around 38:00) and has whispered something to Fischer, in the next shot the rug disappears.
When Grace Van Pelt discovers their entire CBI unit is also being bugged, the computer screen shows their former CBI ID's. Under Jane Patrick's ID it says "Special Agent", when in fact he was a consultant.
Charles Whitaker is posthumously awarded the National Intelligence Distinguished Service Medal. The medal presented (five-pointed blue and gold star with blue and white ribbon) is nothing like the real medal (16-pointed white and gold star with red, gold, white and blue ribbon).