This episode reveals where unwished wishes wind up; in storage lockers in Fairy World's Giant Storage. It also reveals that Timmy has made so many wishes and has unwished a lot of them that he not only needs a larger locker to store his unwished wishes, but also an entire ISLAND had to be constructed to house his most dangerous wishes.
By yanking The Founding Fathers out of their time period, Timmy accidentally altered the timeline as demonstrated in Twistory. They also weren't wishes. They were real people that Timmy wished into his time period.
Whatever happened to Mark Chang after the unsuccessful battle with the Unwished Wishes? Also, Mark wasn't a character that Timmy wished into existence.
Timmy never wished the sphinx away in Abra-Catastrophe!. This goof is pointed out in the episode.
Super Bike was never unwished, it was flushed down by Super Toilet piece by piece. Many of the other unwishes, such as Dark Laser, the Pumpkinator, and the Great Sphinx of Giza, were either never wished away by Timmy or (in the Sphinx's case) never even wished up by Timmy in the first place.
The Gigglepies can be seen in the crowd of Unwishes, but this is an error as Timmy never wished them up at all they were already around when Timmy first met them.
The bars were set aside too far, so Timmy and his friends could go right through the cage bars.
Pumpkinator's mouth was the same mouth of the one Timmy wished for in Scary Godparents. But in all later scenes, it is the same one in the Crash Nebula cartoon.
In this episode, undone wishes are transported to Unwish Island (which is when there is no more room for the godchild's locker for unwished wishes). However in Timmy's Secret Wish!, it was revealed to be Hocus Poconos. It is possible that there might have been too many wishes on Unwish Island by the timing of Timmy's Secret Wish, so the rest of the undone wishes might have been moved there.
Despite being in Unwished Island, Gary was never really unwished.
When Timmy said "We reek!", the captions display the second E in REEK as an A, and include a W at the beginning of the word, thus displaying Timmy's quote as WE WREAK!.
Sanjay's mouth and nose look different when showed in the cage in the VCR where Gary explains what is going on.