I have seen this as well.  It does update the numbers once the unit passes through a city, but the numbers need to have been correct from the beginning.

To explain it more verbosely: When you have a unit selected and you mouse-over a tile, the movement path preview shows up, and if you have a city along that path, the instant movement through the city is ignored when calculating the number of turns to get to the destination.  So, if my unit would pass through 3 tiles of city, it counts those as regular plains tiles towards its estimation of how many turns it would take to get there.