When you sell Trade Goods in port cities, your ship(s) will carry back Silver profits from trading.

For trading, your Silver will be used immediately when you buy Trade Goods, 

but your profit will be received later when your ship arrives at your Territory, in case you sell Trade Goods.

Also you can only receive as much Silver as you can store,

which means that if you make more Silver than you can store in your Depot, your surplus Silver will disappear.

You can either upgrade your Depot before your ship arrives so you can store more Silver, 

or you can use your Silver to make room.