Case 1: Different water colour
In the Beta, the water palette in Tidal Tempest is a different colour. Notice how the colour of Sonic is the same as when he is above ground. There is also a foreground ripple effect like the Japanese version of Sonic 1 (not present in this screenshot as it was taken with an earlier version Ages).
Case 2: The elevator object
In the Beta, there is a platform that moves upward when you stand on the button. In the final edition, there is a spring instead.
Case 3: The Escalator
In the beta, there are escalators that move up some slopes in the level. In the final edition, there is only one of these block that moves up the slope.
Case 4: Badly coloured waterfall
Notice something wrong? The waterfall is coloured wrong with no palette cycling.