When Bill and Ted tell Socrates in his original time, 410 B.C., that they're dust in the wind, Socrates says, "Yes! Like the sands of the hourglass!" Although the joke is that he's unknowingly quoting the opening of Days of Our Lives, the hourglass was first introduced in Europe in the 8th century A.D.
During the water slide sequence, Napoleon appears to be wearing modern underwear underneath his historical undergarments. He could have somehow acquired these undergarments during his time in 1988 San Dimas.
In the saloon fight when Billy the Kid is caught cheating at cards, a prostitute swings in on a rope and takes a guy through a window with her. The rope she swings on disappears and re-appears a few times between shots.
After the "gum and cans" repair done to the booth's antenna early in the film, some later shots of the booth show an undamaged antenna. This is most noticeable in the "Circuits of History" as well as the presentation at the end of the film.
After finishing their History Presentation and returning all the Historical Figures to their own time periods, Bill and Ted are back in the garage filming a rock video and the Time Machine is shown standing outside the garage door.
Minutes later there is a flash and Rufus arrives with the Princesses in his own Time Machine, but when the garage door is opened there is only one Phone Booth standing there when there should be two.
Napoleon looks at and tries ice cream as if he's never seen such a food. In reality, ice cream had been around for generations prior to Napoleon's existence and in fact, Catherine de Medici introduced the French to ice cream when she married the future King Henri II over 250 years prior to Napoleon's reign. Being a dessert of the elite, Napoleon more than likely had ice cream before his time travel to San Dimas.
At the beginning of the final report, Billy the Kid shoots out a light with his gun, despite having just been broken out of jail, where the police would have undoubtedly taken his gun away. However, the final report portion of the movie includes all sorts of props (couch for Freud Dude, swords for battling Miss of Arc, keyboards for Beethoven, etc), so it's safe to assume that future Bill and Ted got Billy a gun for the presentation when they came back to set everything up.
When we see the phone booth being formed and there is a reflection of it in Rufus' glasses, we can see that the "reflection" is just a photo of the booth as the text at the top of the booth is NOT reversed.