I don't know if this is an bug or intended, but in the Mission War is good for Business to be able to scan a Ship you need to completely stop your vessel. Nothing Gamebreakibng, but very inconvenient until you figure that out, as you normaly can scan things "by the fly".
I have also had this same problem with both Trading Treasure Station and War is Good for Business. Submitted tickets for both. I found that when Mok's health gets low and you stand close to him you will get a dialogue button. Click the button and he will stop fighting. I did not submit a bug report for that as I though it was a fluke.