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, as questions or make any further accusations).
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.
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 Bill and Ted are playing Twister with the Grim Reaper, Bill has his left hand on red and his right hand on blue. However, in the next shot as the Repear moves to "right foot green", Bill's hands have switched places, with left hand now on blue and right hand on red.
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 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.
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.
The goof item below may give away important plot points.
Death has been unable to collect souls because he's had to play Bill and Ted at Battleship, Clue, Electronic Football, and Twister. And because Bill and Ted has won, Death is now at their command, further preventing him from doing his job (when Death has been challenged in the past, he was unable to do his job then as well). Yet when the trio arrive at Heaven, other souls are arriving there also. In "real life", the other souls would not be dead; Bill, Ted, and Death would be the only ones arriving at Heaven.