If you're missing items, college/university specialists, goods or coins, there are three most likely explanations for that:
1. They have been used in a quest
If a quest requires you to "Spend" the items, goods, coins or even specialists, this means that upon tapping the "Spend" button, they are consumed toward the quest. "Spending" something this way is irreversible.
2. They have been used to produce something else
The most common misconception concerns Cargo Port items and College graduates.

For example, Cargo Port can produce Planks, but Planks are also used each time you produce Wooden Beams. This means that 3 Planks will be instantly deducted when you start the production of a Wooden Beam.

The same goes for College trainees. E.g. you can train a Designer in College, but if you decide to train an Engineer at the University, 1 Designer will be used, i.e. disappear from your inventory along with 1 Mechanic.
3. They have been used to put out a fire
This only applies to Water units.
99% of the time the reasons above explain the disappearance of the items, goods, or coins. However, if you are absolutely positive that an error has occurred or if you need confirmation from our support team, please feel free to contact us for detailed information.

If you need to produce some item or a specialist and the layout is gray, though you have enough resources, it means that your inventory is full and you need to free some space first (use the items in quests) and then you can start producing them anew. 

In case you’re experiencing any other issues, please contact us and let us know.