When you initially place a building (and there's more than one spot to put it in) the UI almost always it puts it somewhere else, and you have to delete the building and re-place. (The only current ways to get around it are to make sure it's on the right spot, scroll off the screen and click Build, or hold down the Space Bar (I think) and then place it.)
Whereever you initially place a city building should be the place where it gets built, and not magically scroll somewhere else and build it there. 
Best regards,
Steven.
