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".
Bender's a convicted felon, so he may have done something in between the episodes that made the orphanarium revert back to its original name and drop all connections to Bender.
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 problems ill effects to speak of.
This can be explained. In this episode Bender is shown dumping a lot of waste, such as the toxic by products from the Professor's nose creation/decryption machine, into the sewers. The toxic material now in the sewer water (as well as other waste) could explain why the water can mutate living tissue as of "Leela's Homeworld", whereas it didn't when Fry fell in during "I Second That Emotion"
In "Space Pilot 3000" Leela states that she is the only cyclops 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...
When the camera pans along the wall showing the orphanarium alumni pictures the last one is titled "Successfully switched from heroin to methadone". In the next shot it disappears and gets switched with the one titled "Often seen in the background of news spots".
It is possible that this was intentional as part of a background joke.
In the episode Fry and Leela's Big Fling, Leela clearly states that the only way she can take off her armband is to sever her arm. She appears to slide it off without a problem.
