Here are some more that were deleted from Errors and Inconsistencies. I haven't included the one about the Time of Enlightenment, because it was incorrect.
Where is Sanctaphrax's fire brigade?
In The Curse of the Gloamglozer, the Palace of Shadows in Sanctaphrax catches fire. Though the populace assemble nearby to watch the blaze, there are no attempts to douse the flames, and the lowly caretaker Tweezel is left to rescue the High Academe. This is despite the fact the Palace is depicted as being very close to the buildings around it, meaning the fire could potentially have spread throughout the city.
Where did the Rock Demons from the Rook Trilogy come from?
In a ravine in Screetown, there are creatures called Rock Demons. Where were they before Screetown was created? It is highly unlikely they were already underground in Undertown.
If there is a ship called Great Sky Whale - is there also an ocean in The Edge?
In Cloud Wolf - Quint, Wind Jackal et al participate in a famous battle with Great Sky Whale - however no mention is made of where a whale might live, were it to exist in Edgelife. There may be some whale-like creatures living in the Edgewater River or in the Four Lakes.
What happened to Woodfish and Goom?
In Weird New Worlds, it is Woodfish who saves Forden Drew, Goom having wandered off to a Great Convocation. But in the Cade Saga it's Goom who saves Cade and Woodfish is not even mentioned. Did the authors just forget about him because he 'already died' in the parallel universe that is WNW or will he reappear in The Descenders?