So, what is your suggestion then? Just an objection to something
Unrealistic behavior is enough to object.
but no suggestion on how to fix it
Simply let Newton laws do their job. Remove the code countering the container's linear and angular velocities. Containers shouldn't have pilot-assist-like behavior !
or how it would add value to the game?
Not only it adds to realism, but there is a gameplay implication. You need a precious container and you fail to scoop it correctly. Instead, you hit it, giving it velocity. If you desperatly need it, you'll have to align your linear velocity with it, making it harder and a bit more challenging for your second try (switching off ship's pilot assist may be an advantage here). I find this pretty good for gameplay -> be careful not to miss your first try.
In fact, strictly, a container should already move the first time it is found (ships debris too by the way) depending on how it was ejected in the first place. But I think we can accept it initially standing still, at least until something hit it somehow.