I'm on the second mission where you learn how to make food. I have two farms, the granary is full and I have two markets but it says they all gather their own food? The markets have food as well so I'm not sure what is going on.

Ah, I didn't realize they needed water as well. Thanks.

No problem! I only just realised my post was talking about Pharaoh and not Caesar 3, my bad: just corrected it, my apologies :)

Make sure the market has enough employees. Screenshots or video links of what you are seeing would be most helpful. :)

I figured it out actually. Embarrassingly enough, I was unaware that you had to place houses in groupings of 4 to advance to more sophisticated estates. Once I began building in joined rows of two, the problem mostly resolved itself, although some houses still resist.

Wells are undesirable structures. Try building reservoirs and replacing your wells with fountains (which, in addition to being not undesirable, provide better water). Build gardens if desirability still needs to be improved.

If you right-click on any dwelling, it will tell you exactly what's stopping it from upgrading. If you have a market full of food and a tent that can't evolve for lack of food from a local market.... then the market probably isn't local enough.