Running Low on Limestone

In the end of the day, the game is a freemium and they need to make money somehow and they decided to limit Limestone so you either grind or buy material packs with real money.

But to answer your question, there's no sure-fire way, you just have to pray you get jobs that give Limestone.

You probably already know this but Limestone drops from Wooden Chests, from Vases and Skeletons during Jobs.

To extend on Xander's answer:

You can also build the workshop after your town has reached level 3. The workshop will provide a random set of materials that you can buy for a price. Since gold is easier to get than materials, this is also a good way to stock up. As you level up your workshop more items will become available for purchase.

You also have the daily reward that gives chests and resources.

Not only that but you get rewards from doing the abyss. I've seen limestone, copper, iron, chests and more.