Paul Krugman argues that the bilateral trade position is irrelevant.

And he summarizes potential explanations:

… one theory of imbalances is macroeconomic: countries that save more than they invest will run surpluses, countries that invest more than they save will run deficits. …

But … [t]he bilateral imbalance is a lot bigger … The other story … is about “triangular trade.” Here’s my version: think of a world containing three countries, Spendthriftia, Austeria, and Petrostan. The first two mainly sell manufactured goods, which are differentiated products so there’s a lot of two-way trade. The third sells raw materials, which it trades for manufactures. However, Spendthriftia also produces a lot of raw materials, e.g. by fracking, which makes it relatively less reliant on imports. What we would expect to see here, even if each country’s overall trade was balanced, would be a pattern of bilateral imbalances: Austeria running a deficit with Petrostan, Spendthriftia a surplus with Petrostan, but Austeria running a surplus with Spendthriftia. …

… [Moreover] I suspect that part of the US-Germany bilateral imbalance is an optical illusion, brought on by transshipment. … we do an awful lot of trade with the Netherlands, and we run a huge surplus in that trade … Surely this represents US exports unloaded at Rotterdam or Antwerp and then shipped on to other EU destinations, including Germany. I’m not sure why German exports to the US don’t go the same route …