I had a contract to retrieve a part from Minmus orbit. (KPBS K&K Ground Base). Since the ground base was small enough (200L/600kg) I just stuck it in the ship's inventory. As soon as it went into inventory the contract failed due to the part being destroyed. The part is still in the inventory.

This is a low priority, you could consider this to be just a limitation of KIS. It's the first time I've had one of these contracts that was actually small enough to just stick in an inventory.

This issue was raised before. Alas, it's not clear how this issue can be fixed (and can it be fixed at all). The contracts system traces the part destruction event, and part has to be destroyed when stored in the inventory.