Can you post any way for others to confirm and/or replicate? See https://forums.elementalgame.com/415301 for details on how to report an issue.

Hmm, I've got a case of a just-captured city with *more* resources than it should have, a total of 11 (city of Imperium, just captured from Yithril, who had earlier captured it from Magnar.  City details window says tile yields: 2 essence, 3 materials, and 6 grain).  Lacking other information, I would guess that this is caused by the same underlying bug, where tile yields are somehow getting changed after cities are built.

https://dl.dropboxusercontent.com/u/89188843/LH_1.0-bug-tile-yield.EleSav

https://dl.dropboxusercontent.com/u/89188843/LH_1.0-bug-tile-yield-debug.err

If it says "base grain/production" etc. than that is the amount without including external sites.  I think sometimes the AI's cities are modified to be better, and can exceed a total of 9 (which normally is not possible within the vanilla game).

Just confirming this is still present in v1.1; I've found both towns with more than 9 total base resources, and towns with 0 base resources in a new game started in v1.1

I've had boosted AI capitals on Challenging difficulty too.

I've seen this as well in my current game.  My game was started in v1.0, but I hadn't taken the city until after the upgrade.  Also, I don't see it listed as fixed in the v1.1 changelog, so it's fairly safe to assume it hasn't been fixed.