Continuity mistake: In the beginning where Indy is young, he fights some guys on that zoo train. When he's on the crate with the rhino in it, the background changes in each shot. Once there are trees behind and a split of a second later there are rocks, once there's a cliff and once a plain, and it all changes in splits of seconds as they change shots. (00:07:25)
Continuity mistake: When young Indy (River Phoenix) is advised by the fedora-topped henchman at the end of the chase, the cut he received while using the bullwhip in a previous scene changes angles. This is a flipped shot, note Indy's backwards shirt. (00:08:25 - 00:11:45)
Continuity mistake: In the beginning, when Indy is fighting aboard the Coronado ship, the very first time we see Indy in this scene (before we see him get punched), he is bleeding from the right side of his mouth. Throughout the remainder of the scene, he is bleeding from the left side of his mouth. (00:11:50)
Continuity mistake: When Indy takes the mail out of his pocket in the beginning of the film, he keeps the "Grail Diary" in his hand, but puts the letters down twice. Once before he opens the package and once after with the wrapper. (00:23:00)
Continuity mistake: In the library scene Indy discovers the "X" high up on the balcony. The X is green with a grey background. When he breaks the tile to find the tomb the X has become a faint outline on the floor. (00:27:40 - 00:28:45)
Suggested correction: You still can see one "leg" of the X on the floor, it's only darker than viewed from above because the camera angle and illumination set used.
I think it is meant to be an optical illusion.
The "X" is first shown as a dark green "X" on a beige background. Next, we are shown the same dark green "X" that is barely visible over a green background. I think we are meant to understand that the beige square tiles were lifted away in a cut scene.
I see no reason why they would replace the floor just for the higher shot, it's the same floor throughout the scene. When they enter it's the same floor we see later as they are going into the hole. It's probably not a real marble floor, so they can use a styrofoam or plywood tile that Harrison can lift, one that matches the surrounding tiles. They don't shine as much as the rest of the floor. In the shot up high there is different lighting, so that could explain it. It just appears to be different. Of course, sudden different light can be seen as a revealing mistake.
Suggested correction: Not a mistake, just a different viewing angle.
Continuity mistake: In the catacombs underneath the library, when he find the "X" on the wall, he is shown ramming the wall twice to break through. The first time he rams it, however, the wall looks as if he had already had a few goes already. (00:31:55)
Continuity mistake: When Indy and Elsa are wading in the petroleum looking for the knight's tomb, Elsa unbuttons and opens her jacket and starts to take it off. In the next shot she opens her jacket and takes it off again. (00:34:15)
Continuity mistake: During the boat chase/fight in Venice, the rear of Indy's boat gets shot up and starts smoking and spouting flames and the engine starts chopping. He leaps onto the pursuing boat, fights until that boat is destroyed in the rotors, then leaps with the Grail protector back onto his original boat with Elsa. The boat is now running perfectly. (00:38:50 - 00:39:55)
Continuity mistake: When Indy and the protector of the Grail are in the boat about to be destroyed by the rotors, there are panels on the top of the boat that pop up and are destroyed when the boat is moving backwards into the rotors. In the next shot, they are intact, then in the next shot, they are destroyed again. (00:39:20)
Continuity mistake: In the speedboat scene where Dr Schneider rescues Indy and Kazim from the boat that is chopped up by the propeller of a ship, she driving the speedboat with the steering wheel on the right-hand side. Seconds later as she drives the speedboat away, the steering wheel is on the left-hand side, obviously a flipped shot. When the speedboat slows down to allow Kazim to alight at the jetty, Indy is at the wheel which is now back on the right-hand side. (00:39:55)
Continuity mistake: After Indiana and the Protector of the Grail escape the boat being chewed up, and the Protector reveals who he is to Indiana, watch his chest area... When Indiana asks "Who are you?" he is looking down at his chest (looking at the tattoo), and when we cut to Kazim you can tell he is holding his shirt open showing Indy the tattoo. Then when we cut to Indy and back to Kazim, his shirt is closed and he then opens it to show Indy the tattoo. (00:40:15)
Continuity mistake: While Indy and Marcus are in the apartment in Venice, after Marcus says, "He knew everything, except the name of the city", he slams the diary shut. Then it's shown open, and he closes it a second time. When Indy takes it, it's once again open. (00:42:15)
Continuity mistake: When Indy is rescuing his father from Brunwald castle, he uses his bullwhip to smash through the window of the room his father is kept in...but in the time it took to jump into the room and get smashed over the head by his father, the bullwhip he used would have lost lots of its momentum and it wouldn't be waiting for him to grab it and use it later on the movie. (00:47:40)
Continuity mistake: When Sean Connery drops his lighter while trying to burn the ropes, the lid is flipped to the right. When he blows on it the lid then changes position slightly relative to the pattern on the rug, then when the rug catches fire the lid's suddenly flipped completely to the left. (00:56:40)
Continuity mistake: By the border, when the German soldier's been knocked off by Indy and his bike rides alone, he suddenly disappears from the side of the road. (01:02:10)
Continuity mistake: When Indy and his father are being pursued by German soldiers on bikes, right after they break through the barrier, the barrier guard comes out of his post and waves the pursuing German soldiers to slow down in the background. In the next shot he's no longer there, and the barrier's quite far away, then in the following shot he's back, and Indy's not so far from the barrier again. (01:04:35)
Continuity mistake: When Indy meets Hitler, there is a shot over Indy's shoulder that shows his lips are slightly parted (relaxed). Cut to Indy's face and he closes his mouth tightly. In the very next shot, with no elapsed time, we see from Indy's shoulder again that Indy's mouth is relaxed as before. (01:10:15)
Continuity mistake: Inside the zeppelin when Indy and his father are talking at the table, notice the white handkerchief that moves all around the table. (01:13:50)
Continuity mistake: When the zeppelin is shown turning around, the biplane that the Joneses are about to escape in is nowhere to be seen. (01:16:10)
Continuity mistake: At one point Indiana's father blows the tail of the plane in which they were flying to pieces in an attempt to shoot at the Germans. This is obviously in a close-up studio shot. The next moment the plane is shown flying in the distance with its tail still intact. (01:17:45)
