That happens when a trade partner captures another trade partner's capital. Sometimes it corrects itself, and other times it doesn't.
For e.g., in one pre-patch campaign it happened when when Russia lost Moscow to Sweden. Sweden appeared twice on the trade list, and the route was still to Moscow. It wouldn't correct after the Russians took back Moscow, so I had to cancel the trade agreement - I was losing money.
IIRC, something similar happened in my post-patch French campaign, but it corrected itself. I would have to load it up, and see, but I think the Russians already took back Moscow.
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