This is not a bug, but rather one of the peculiarities of the wolphax, due to basically only their super noble and honor focused knights are up in space, alone on their ships. Just like not raising your shields when contacting a knight will lower your reputation for them (because not raising shields is interpreted as you not considering them a risk for your ship at all, which most wolphax knights disagree and are insulted by), the fact that knight Marshalls immediately jump to the rescue of any "slave" they see in your cargo bay is based on that lore.

game design wise: nothing else except the compass is contraband in a wolphax scan, unlike other alien races which each take issue with a variety of different items you could carry.

This is one of the mechanics of the game, due to the different seeds and therefore different aliens, one has to adapt their strategy when doing different quests. Finding out these bits of information about the races throughout the game is at the very core of making progress.