I agree that market and university might be confusing at the beginning. This is due to the fact that I hit my own soft deadline and had to publish game before being able to work on it further. I will definitely change their mechanics to more transparent one later. For now I plan to add gardeners/florists that will collect berries/flowers for city and change requirements for respective researches to be reachable without market manipulations.
Purchase from market, on the other hand, takes resources from warehouses. So, if market restocks with 10 stones, and warehouse’s level of stone reaches, for example, 8 stones, you won’t be able to buy 10 stones, only 8 will be available and buying them will reduce city’s stone level to 0.
I want to make economy vital part of the game, so player could have many different ways to earn coins to avoid activities he don’t like by simply buying stuff from the market. But yes, this feature is vague right now, due to the lack of side content. This is why I want to add more side content in next updates, rather than focusing purely on story progression.