I had this happen twice to me in my most recent game, and figured out why both times:
A.) Another civ built a city on top of a road going between two somewhat distant cities of mine. Since I didn't have any units in the area of the city, I couldn't "see" it until I sent one down the road. I had to take the city to get the trade route back.
B.) Another civ pillaged an iron mine that belonged to a city-state than I was allied with, thus cutting them (and me) from its uses. I had to wait for the city-state to rebuild the mine, which took quite a while.