When Death falls from the sky after Bill and Ted are resurrected, he hits the ground wearing black and white shoes, when he had been always seen in bare feet.
In Bill and Ted's Excellent Adventure, princess Joanna, ends up with Ted, whereas Princess Elizabeth ends up with Bill. However, in Bogus Journey, Ted is with Elizabeth and Bill is with Joanna.
When Bill and Ted are in Hell and their floating rock is being pulled towards Satan, Ted can be seen holding a hammer, when he didn't have one before when he and Bill fell on their rock. This was from a deleted scene in which Bill and Ted were forced by a demon guard to break rocks.
At the Battle of the Bands, scorch marks suddenly appear on the evil robot heads shortly before Bill and Ted throw them away. This is from a deleted scene where DeNomolos fires at the boys; but they use the heads to block the shots.
When Elizabeth and Joanna are being knocked out, a heap of clothes appears on the floor behind them. This is from a deleted scene where the evil robots dress up as each other.
When Bill and Ted are playing "Clue" with Death for their souls, Death makes an accusation in an attempt to win the game. In order to see if his accusation is correct, Bill and Ted check the contents of the envelope. This is in violation of the rules of the game. After an accusation is made, the player who made the accusation, and that player only, checks the contents of the envelope. This way, there is no way of the other players knowing the correct answer should the the accusation be incorrect (in which case, play would continue as usual, but with the player who made the incorrect accusation no longer able to roll the dice, ask questions or make any further accusations).
Bill & Ted are playing as a single player, essentially making this a two player game. It would not matter who checked the cards, either way the game would be over. With his guess, Death would have either won or loss.
When Bill and Ted are being escorted out of their apartments by the Evil Bill and Ted robots, the face of Ted's double is briefly visible.
Toward the end of the film, during the montage of newspaper/magazine covers that reveal world events that occur due to the influence of Wyld Stallyns, the final headline makes the announcement that the band will play Mars 'Station'. However, this image is superimposed on a false-color rendering of the planet Venus. This may have been played for intentional comical effect, given the 'clueless' nature of the duo, though it is likely just a mistake.
When Evil Bill removes his head and throws it at the basketball hoop, the actor's real head is visible.
When Satan pulls a lever to bring the rock with Bill and Ted on it closer to him, the seam on the leg of the actor's red bodysuit is visible.
When Bill, Ted, Death and Station are shopping for parts to build the robots, the amount of items they put in the trolley don't match up with later scenes.
When Bill and Ted are playing Twister with Death, Bill plays barefoot. His shoes are visible off to the side. After Bill wins the game, Death tells them that he will take them back, and the two talk about how they will fight their evil robot duplicates. Right after they talk, they follow Death, and Bill's shoes are clearly shown on his feet, although he never picked them up after the game.
When Death is falling from the sky after finding Station, his mouth is closed as he screams.
When Bill and Ted are falling to hell and upright you can clearly see the seats they are on to mimic falling. Most visible with Bill as he is wearing lighter jeans/pants. They look reminiscent of unicycle seats.
When Bill and Ted are freefalling into Hell, when they've turned parallel with the ground, supports/suspension equipment is visible through their t-shirts.
When Bill and Ted are walking out of the desert after they "Melvin" Death you can see the shadow of some piece of equipment on Ted when the camera is rotating to show the sign.
In the scene where the aliens join into the big station the support wires that help them into the air are clearly visible.
When Bill & Ted are being led into the desert you can see two different shadows. One from the sun (matching the rest of the shadows), and one cast in a different direction from an extra light source.
When Chuck De Nomolos states to Bill and Ted that he can also play the "time game", (meaning that he traveled back in time to the present to give himself both a key and a gun) he pulls out a key from his pocket. The gun, nevertheless, seems to materialize from nowhere into his hand. It is never stated that such a deed was possible with time travel, as apparently all Bill and Ted did was place the object in a certain location for later use.
Near the end Bill and Ted are still unable to play well enough to win the battle of the bands so they use the phone booth to use time to learn how to play and even have children during that time. It was established as a major plot point in the first movie that this would not be possible as time in the "present" keeps advancing. So if they went off for presumably over a year to practice then the battle of the bands would have been over for over a year before they got back.
When playing charades with Station in heaven, The Reaper names
the movie "Butch and Sundance: The Early Years" when the movie is actually called Butch and Sundance: The Early Days (1979).
When Bill and Ted are playing Twister with Death, Ted spins the arrow and announces "right foot green" while the arrow is still spinning.
When Bill and Ted were playing Battleship with Death, it showed them one hit from winning which means that they've already hit Death's last ship multiple times. They first guessed B3, which is all the way in the top left corner. Then guessed J7 which is all the way in the lower right hand corner for the last hit. There is no reason for them to guess B3 at all when they know that his last ship is around J7.