Raoul is previously shown to have only one ear, but is now shown with both ears intact.
Although the orphanarium was renamed the Bender B. Rodriquez Orphanarium in the episode The Cyber House Rules, due to Bender's gift of twelve orphans and a Government check for twelve hundred wingwangs, it seems to have reverted to the original name "Cookieville Minimum Security Orphanarium".
In this episode and others following it, it is stated that the water is so toxic that it will immediately mutate any creature that isn't already mutated; however in "I Second That Emotion" Fry is submerged entirely in the sewer liquid after being set free by one of the natives and emerges without any ill effects to speak of.
In Space Pilot 3000 Leela states that she is the only one-eyed alien on the entire planet. Leela's parents also have one-eye. But, it is possible that this is not really a goof because she might have not known. In fact it definitely is not a goof because this entire episode revolves around Leela not knowing who her parents were and she clearly states in Space Pilot 3000 that her parents abandoned her on earth, making her the only one-eyed 'alien' on the planet...