Please, keep in mind that there are several quests in the game that require saving coins, goods or items. Note that if a quest requires to use money, goods or items, they will be deducted (see example below). If a lot of coins or goods or some of your items are missing, that probably means that you have completed one of such quests.
The same also goes for College/University specialists. In this picture 5 Builders will be deducted after clicking 'Use':
Cargo Port materials are used in various quests, but they may be also used to produce other materials. E.g., 3 Planks are consumed to produce a Wooden Beam. The picture below shows which materials are used to create items in the Port:
Pens and Textbooks are used to train the specialists in College. These items will also be deducted once the training starts:
Meanwhile, Builders, Mechanics and Designers are deducted too, if you decide to train University specialists. See the picture below: