In this case, come and go are usually related to some baseline reference. Go means it is moving further away from that reference while come means it is moving towards the reference, just like with directions.
With the example of prices: A reference price you are talking about might be the price of coffee right now. In the future, prices can "go up" and increase, or "go down" and decrease. In both cases the price of coffee is moving away from the current price.
Once the price of coffee "goes up," it can then "come down," meaning the price lowers towards the reference price. The opposite can happen, where it "goes down" and then "comes up".
This baseline reference price can be many different things: the current price, a desired price, or a price at some time in the past are all references.