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.
Factual error: When Bill and Ted grab Beethoven, we are shown the piano he was playing which is a Steinweg (Steinweg later changed his name to Steinway when he immigrated to the United States). Steinweg made their first piano in 1835, and the model shown was built in Braunschweig so must have been made after 1858, but Beethoven died in 1827, years before a Steinweg piano existed. Also the onscreen graphic says it's 1810. (00:47:50)
Continuity mistake: At one point, when they time-travel away from "1,000,000 B.C.", Bill is on the left inside the phone booth and Ted is on the right. When the camera switches away, then back, they've changed sides.
Continuity mistake: When Napoleon first comes back from France and he's hanging in the tree, he disappears when the camera angle changes to an aerial view of Bill and Ted.
Other mistake: At the Circle K when future Bill and Ted have finished talking to present Bill and Ted and go back into the phone booth, where are the other 5 historical figures? Especially as it is emphasized that they are all squished together, when they land you can see Beethoven, but he isn't there at the end when they leave.
Continuity mistake: In the beginning, when Bill and Ted are at the Circle K and the phone booth lands with their future selves in it, you hear Bill say "Aw, I hate that part" just as they land in the booth. At the end when we see them land to talk to their past selves, Bill doesn't say that.
Revealing mistake: At the end, when all the historical figures are going back into the phone booth, you can see the trap door in the back open and the people go through it. It would be kind of tight to fit all of them in the booth at the same time.
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)
Continuity mistake: During the classroom scene, the spelling of of Genghis Khan's name on the chalkboard changes from "Genghis Khan" to "Ghenghis Khan" between shots. (00:04:50)
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.
Character mistake: Gengis Khan has been 'kidnapped' by Bill & Ted in the year 1209. Yet in the final report, they say that they picked him up in 1269.
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.