Factual error: When Matt Damon steals the brief case and reads the memo listing the Nazi party members - the title of the memo is set in Arial which wasn't available as a font until 1982. Furthermore, the memo looks laser copied rather than typed. The fact that this is a closeup wiew makes this a rather obvious mistake.
Other mistake: During the 25 years time span of the movie, all of the characters age noticeably except for Clover and Damon. He, miraculously, goes through his teens, 20s and up to his late 40s gaining just a couple of gray hairs and a few wrinkles around his mouth, plus the same young voice from the early days.
Plot hole: Near the film's end, when Edward Sr.'s son, Edward Jr., is about to be married, Edward Sr. approaches his son looking very grim. He is about to tell his son that his fiancee has died. At this key moment, Edward's wife exclaims to her husband, "What have you done?!" Logically, this does not make sense, since Edward's wife, Margaret, has no knowledge (as far as the audience knows) of the Bay of Pigs leak made by her son, nor of her son's fiancee's spy role in obtaining the information. Without knowing this information, Margaret would have no reason to suspect that her husband was involved in some bad incident involving her son's fiancee.