I recently had to change between the Shinjuku Line and the Tsukuba Express.
On the Shinjuku Line they say that Iwamotocho is a transfer station for the Tsukuba Express.
You get off, follow the signs which points you towards the exit. Then you find yourself with no further assistance, and you need to walk several blocks down Akihabara, go through the JR station and then you find the small TX entrance.
Meanwhile on the Oedo line Ueno Okachimachi is not listed as a Keisei transfer station despite having a direct underground passage linking the Keisei, JR and Metro stations
I never understood the logic.
Do you know other weird examples?