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.
It's not just the viewing angle. The "X" is gilt-colored and bright but becomes extremely muted, almost a shadow when viewed at the lower angle. Another possible reason for the different appearance is the patterned perimeter. It too appears to be a very different color and muted. It's possible that in post-production, the scene processing done by the cinematography team adjusted the lower angle scene for a change in light levels due to close-ups, the time of day, or some other factor.
Continuity mistake: When Sallah pulls his rifle and overtakes the Nazis at the Great Seal he is in the forefront with the Nazis in front of him and Indy and his father are behind him. Within the next scene he is now in the background with his rifle resting in his arms.
Other mistake: In the fighter plane scene, their hats don't blow away.
Revealing mistake: The seagulls on the beach (when Dr. Jones scares them with his umbrella) are blatantly fake. They don't move an inch. This was also confirmed by producer Robert Watts in this making-of video https://www.youtube.com/watch?v=BMFMKsrXuGY (minute 2'30").
