Other mistake: When Alex, Marty, Gloria and Melman are talking together inside the boxes, Alex has three holes in his box allowing light in for him. Melman, Marty and Gloria have that too, but Gloria's box is lying under Alex's and Marty's, so it can't get as much light - but it does.
Suggested correction: When we see the outsides of the box on the ship we can also see little gaps caused by wood planks nailed to the sides of the box so there should be a little light coming from in between to Gloria's box holes.
Continuity mistake: When Alex tries to get Melman out, he is lying near the sea, but when Alex tries to get him out with the tree, he is farther away from the sea.