As noted in the bug thread this has something to do with the delayed responses, refer to that for more info. Look at your Tech Screen, stone roads will be marked as Cataloged. If they are not and you can build them then there is another kind of bug happening there. I looked and they are set to 2 food, so something else was a foot. When you add a unit to a city the AI will shift around units if they are not locked so this may have happened. However, Nobles costing more food would be a good idea, especially under Feudalism Civic, and other Units could be looked at as well for this. Well do keep this in mind. You can tinker with all the settings yourself in the CivicInfos if you feel it needs rebalanced and give us feedback on any changes you think works best.