First, off, how many facilities can you think of with 36 holes of consistently high quality golf? Royal Melbourne and Winged Foot come to mind. But think about the two courses at Winged Foot. They share the same property and holes often run parallel to each other, but, with some exceptions, few would confuse a hole on the East course with one on the West. Much like the design of an individual hole, a 36 hole facility must provide options.
As far as courses that just don't seem to belong to their environment, I'd say most attempts at "links" design that are plopped into the midwest. Some can get away with it because those lands were historically prairie, and the contours of a constructed golf course can mimic that history, but most come across as simply pushing dirt solely to create corridors for play. For example, I actually enjoy both Purgatory Golf Club outside of Indianapolis and the Kampen course at Purdue, but neither, in my mind, seem to fit the land.