From the Harbour FAQ on BGG:
When using warehouses, how many goods can you store?
You can keep up to the number of goods you have warehouse symbols. However, you cannot use warehouses to increase the amounts of goods to higher than they were before shipping.
Example: You ship two stone and four wood and have three warehouses. You can save two stone and one wood, one stone and two wood or three wood. You cannot "store" three stone since that is more than was shipped.
Based on this, you are allowed to store multiples of the same type of good, you just can't store more than you currently have (i.e. no making things out of thin air.)