Right before Miss Piggy takes on the agent, he takes his glasses off twice.
Rizzo loses his cap during his fall into the rat cage. When he and the other rats first talk to Dr. Tucker, Rizzo is wearing the cap again with no explanation as to how he got it back.
The yellow spyglass prize from the cereal box is in Gonzo's hand in one instant, then back in the cereal bowl in the next.
In the opening shot of Noah's Ark, the loading door is near the bow. When Gonzo tries to get through the door, it is closer to the stern.
When Gonzo first puts his hand on the spyglass, it is near the middle. In the next shot, his hand near the end and the spyglass has extended itself.
When the space ship is blasting off at the end of the movie, the exhaust from the engines are going up and INTO the rocket engine, not down. Obviously they reversed the film of it landing to make it seem like it is taking off.
As Rizzo is dangling from the bedroom window, he says to Gonzo, "No, I'm Santa. But I forgot my reindeer," without moving his lips.
When Bunsen is demonstrating his new inventions, and he turns around and walks to the table, his puppeteer is visible below.
One of the "R U There" messages is shown in Hollywood, California. Later, a globe showing the spiral formation of the messages has the western most portion of the spiral east of California.