Other mistake: Beethoven didn't seem fussed nor resentful of Napoleon being part of the group. Historically he temporarily admired him and wrote the Third Symphony inspired by Napoleon's ideals of Europe's new hope of enlightenment but later despised him after he crowned himself Emperor of France in 1804 and furiously scribbled out his name off the title page of his Third Symphony and named it Eroica which he originally titled it as "Bonaparte Symphony" due to his former admiration of Napoleon.
Character mistake: In the movie they grab Genghis Khan in 1209 which would have been correct, he ruled Mongolia from 1206 to 1227. In the presentation at the end they say in 1269 he did this and that, that would have been Kublai Khan's reighn of terror in Mongolia.
Suggested correction: Bill and Ted have proven not to be that smart. Easy for them to get those things confused.
Factual error: When Bill, Ted, Billy the Kid and Socrates end up in the future, Billy and Socrates are told to stay in the phone booth. Socrates nods and remains in the phone booth. In Greece, nodding means no.
Continuity mistake: When the 2 girls at the mall leave after calling Freud a geek, the girl in pink puts her purse strap on her shoulder. In the next shot, it's off her shoulder, and she's seen putting it on it again.
Audio problem: When Bill, Ted and the other historical figures are getting Sigmund Freud into the phone booth, in a shot shown from outside the window looking into the booth, Freud says "What are you doing", but his mouth isn't shown moving along with the line. (00:47:13)
Factual error: During Bill and Ted's first time traveling in history, Rufus states they are in Austria in the year 1805. 1805 was the year Napoleon achieved his greatest victory over Tsar Alexander I and Mikhail Kutuzov at the Battle of Austerlitz (present day Czech Republic). Napoleon didn't invade Austria until 1809.
Suggested correction: Austerlitz was part of the Austrian Empire. But that battle was after the Battle of Ulm. After Ulm surrendered, Napoleon advanced to Vienna and took the city. The Austrian War did occur in 1809, but that was Austria attacking to free neighboring countries under Napoleon's rule.
Plot hole: It seems that after committing 6-odd counts of aiding and abetting, literally right in front of the strict Police Captain father of one of them, Ted and for that matter Bill, would be lucky to only go to military school, regardless of passing or failing one particular class.
Suggested correction: The threat of Ted having to go to the military academy in Alaska was because he was going to fail. Since they passed and graduated, there's no need to attend the military academy. Some time passes before Rufus brings the babes to Bill and Ted, so we don't know what punishment they were given.
This isn't ordinary misbehavior, it is a felony, what do you think the punishment would be? No TV for a week?
I don't have to speculate what their punishment would be. Certainly neither would be sent to military school (which is a TV and movie trope that wayward children get sent there anyways). Your mistake entry is not a plot hole plain and simple.