Well, one exception is 隣 (neighbor). The reason is that both 隣 and 鄰 exist with the same meaning, and 鄰 with the village radical did come first, but for whatever reason 隣 became standard in Japan.
The thing is that basically two different radicals got merged visually. But they retained their original meanings. The village / city meaning one came from this 邑. The one that means mounds / hills looked like this originally 阜.