If I'm docking at the same time the transport convoy is, sometimes glitchy things happen to me, like my average price paid is set to zero, or the game crashes, so I try not to be there at that time. But I don't usually buy hardware anyway. Building isn't really worth it, and there's rarely enough markup per cargo slot to make it worth hauling.
How late in the game is it? By the later game, 3-4 years, when the AI is flush with cash I've seen hardware pretty slim on the ground. My suspicion is the AI sets a buy order and snags hardware at any price and puts it in his storage. You might try the same wherever you have storage.