I hope this is not something I simply never noticed before. After building the town of Gouda I am unable to place a citizen in a square under Gouda's control because a citizen of foreign controlled London is there.

To reproduce build Gouda where the settler stands (near German controlled London). The square to the south of Gouda is "boxed" as used, but obviously can only be used by the Germans.
http://www.civfanatics.net/uploads6/Gouda.gif

Presettlement save (http://www.civfanatics.net/uploads6/PreGouda.SAV)
Save after settlement and exiting city screen (http://www.civfanatics.net/uploads6/Gouda_Inaccessable_Square.SAV)

It has always done this. It will sort itself out on the next turn.