This is for version 3.005 (or whatever version is available on this date).
STV: Have had to skip STV this time around b/c the guide fails to adjust to certain quests not being available.
Navigation: There are many waypoints that are off completely. A good place to start would be SW npcs and the SW flightmaster. Also, not sure of the Menethil Harbor/SW boat change has been reflected yet.
Navigation: Navigation for dungeons is often messed up, notably for gnomergan. When you walk in to gnomer, it says to hearth to ironforge or something like that.
UI bugs: The model viewer will often not show/show correctly, and the guide often bugs out and loses collapsibility and/or the arrow.
I have noticed the severe problems with jumping around in the guides starting at around 40.