There appears to be some memory corruption in Challenge Mode. I cannot reproduce these problems during normal game mode.
What I did: Deploying several ships (tried both with 10 cruisers and with 40 frigates), and giving all save one of them the “cooperative” order, and then selecting every ship.
What happened was (apparently) pretty random. It varied between the following:
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The order list shows all ships having some new order I didn’t give to any of them.
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When clicking on an order in the list (eg. “Vulture”) I got a details window for some other order (eg. “Fire at Frigates”).
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Crash: “GSB.exe has stopped working.”
(Probably not important, but it just occured to me that all ships had some empty modules. I haven’t tried again with non-empty ships.)