"Trade rule prohibits trade with commander".
After some testing, it seems to occur in situation when you have station traders, but trade rule is set to "external" for some ware. Meaning, "Forbid trade with player".
Here's what "External" trade rule looks like.

So, after thinking about it... it seems that when station traders consider trading with someone. They first check permission to trade with seller, an then check if they themselves can trade with buyer. And because station trader belongs to player faction, when trade rule forbids trade with player faction... station trader will be unable to trade with the station it belongs to. And "trade with commander" message appears.
But this is very counterintuitive. The default expectation is that COMMANDER manages the trade. Meaning a station searches where to buy, then where to sell, and issues orders to the traders, an traders follow them. Meaning at no point station TRADER should consider whether it is allowed to trade with commander, because commander is the one making the t rade.
That means that a station set to "external" rule should command its traders to buy from NPC stations. An a station set to "internal" rule, should command its trader to buy from player station. That's the behavior I'd expect. In practice, "External" rule seems to disable traders completely, and it wouldn't surprise me if it is tied to the odd resupply ship issues I outlined earlier.
I provided a sample save. See Atreus Cloud trading station. Multiple traders assigned to it do nothing, while NPCs dock to station to trade.
The reason why I set "External" rule on trading station is because I do not want it to attempt to supply player stations with goods.
https://anonymfile.com/j0N84/quicksavexml.gz
https://www.fileconvoy.com/dfl.php?id=g ... 0b9cc2f8eb