The door of the "Swinetrek" that takes Link outside led to a hallway in earlier episodes.
During the Wild World of Muppet Sports, the goldfish in the bowl is obviously a separately filmed element, as it's fins can be seen moving outside of the glass bowl, first through the table at the bottom and later through the side.
Twice, when Beauregard presses the top of his hammer to the nail, it begins to bend, revealing it to be made of foam rubber. The second time a tear in the foam is even visible.
Beauregard says he told Beaker to get a power saw. However, when Beaker appears he carries a chainsaw.