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.
When Bill & Ted are in Bill's room just before Missy brings them sandwiches, Ted says, "Remember at Disneyworld..." Would they both have gone to Disneyworld in Florida when Disneyland is about 30 minutes away from 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.