Revealing mistake: When Scrat removes the giant acorn in Scratlantis the city is immediately flooded. Everyone in the background, including Scrat, is blown away by the sudden rush of water. However, Scrat's host (slightly off-camera) in the foreground doesn't move and doesn't seem affected by the strong flow.
Continuity mistake: When Scrat arrives at Scratlantis, it is shown that the acorn-shaped island is formed by 3 land masses lined up. However, when Scrat causes the island to sink, a full solid acorn-shaped island is shown sinking.
Continuity mistake: When the pirates sing their shanty they throw sea stars at Sid on each side of him. In different shots, there are three on one side.