The door on the riverboat through which Madame Medusa makes an entrance remains open until right before she arrives, then it's closed and she opens it. This same door was torn and out of place when it was open, when we see it closed, the door is intact and standing perfectly. Then after Medusa opens it, the door falls apart again.
When Bernard and Miss Bianca are awaiting Orville, Miss Bianca first takes off her coat. After she shouts, "Look! Look, there he is!" and we see her through the window, her coat has reappeared, it then vanishes again.
After Nero sends Bernard up in the air by playing a hard note on the organ, Brutus throws himself after the mouse causing all the pipes to go flying, however the one Miss Bianca was in re-stands in the next shot.
After Brutus and Nero, the alligators, have brought Penny back to the riverboat after she tries to escape, we see Nero walking after Mr. Snoops after he's offended them. Nero is holding Teddy on his mouth, but in the next shot Teddy is in Penny's arms.
All throughout its journey across the sea, the bottle traveled without a cork on its opening, however, during the final moments of the sequence we see the bottle with a cork on and finally, we see Bernard struggling to remove it.
After Medusa gets word that Snoops captured Penny with Brutus and Nero's help, she flies the swampmobile onto the deck where Snoops is waiting for her. The next time we see the swampmobile (when Penny, Bianca, Bernard, and the Swamp Folk are staring it to escape Medusa), it's back in the water.
When Penny is first captured by Brutus and Nero, Brutus initially holds her by the strap in back of her dress. In fact, that is how Brutus carries Penny back to the river boat through the swamp. However, when the crocodiles return to the river boat with Penny, Brutus is suddenly holding Penny upside down by her underwear. There is no explanation for how Brutus could have possibly turned Penny around like that without releasing her just for a moment and preventing her from escaping. It even stands to reason that Brutus would not release Penny until he got her back to the river boat. Additionally, when Brutus carries Penny upside down through the door of the river boat, Penny is facing toward Brutus. Yet, in the next shot when the crocodiles are inside the river boat with Penny, she is suddenly facing away from Brutus.
After Bernard has retrieved the note from the bottle at the Rescue Aid Society (RAS) meeting, he falls back into the bottle. The scene changes back and forth while the RAS discusses sending Bianca on the mission.
As the shots change to show Bernard, the rope he used to enter the bottle and was outside it when he fell in now appears and reappears inside the bottle several times.
When Brutus and Nero bring Penny back to the river boat, just as the crocodiles are entering the doorway, while Brutus is holding her upside down, Penny is facing Brutus. In the next shot where the Penny and the crocodiles are inside the boat, Penny is facing away from Brutus.
At the meeting of the Rescue Aid Society we see a delegate from Austria. Not long after we see another delegate from Vienna. Vienna, of course, is the capital of Austria. If the Rescue Aid Society is like the United Nations, then all delegates should represent nations, not cities. More importantly, even if cities were represented, it would make no sense to have two delegates from the same country.
The traffic light that changes (and Orville flies through) has the three standard lenses for the green, yellow, and red phases. However, in typical cartoon fashion, the light goes from green to red without any yellow phase.
In Madam Medusa's pawn shop, the sign on the wall states "Loan Money 1/2 Rates on Diamond's". In this context, "Diamonds" is a plural, not a possessive noun, and therefore does not require an apostrophe.