Most times when players are missing their valuables, it's because these things have been used in a quest or as ingredients for production. The following items get overlooked the most:

If a quest requires you to save some amount of any items, goods or coins, then once you click "Use", this amount will be deducted from your game account!

For example:
After you click this button, 100,000 coins will be gone and the task will be marked as complete.

The similar thing would happen if you clicked "Use" in a task to "Train 5 Builders" or "Save 1,000 goods".

The most "expensive" quests in the terms of spending coins are Snow Station (500,000 coins), Genie (500,000 coins), Mountain Hotel (550,000 coins) and Super Stadium (1,500,000 coins).

Cargo Port materials are used in various quests too, but they may be also used to produce other materials.

For example, one Plank is consumed to craft a Wooden Beam:
Bricks and Reinforcements are consumed too when crafting Concrete Slabs and Metal Beams respectively:

These College graduates will be gone if you train the corresponding University specialists:
For example, if you teach an Architect, one Builder and one Mechanic will disappear from your inventory.

One Drop of Water is consumed every time you put out a fire in your city.

If your quest needs Water, make sure to avoid fighting fires for a while. Don't worry, nothing bad will happen to your buildings, as fires tend to die out themselves with time.

Pens and Textbooks are main requirements for teaching College specialists. Please note, that these items will too be consumed:

Where to get more goods:

You plant items in your farms and make items in your factories to get goods