I am instantiating an object with following code
public Object ball;
Instantiate(ball, hit.point , Quaternion.identity) ;
Where hit.point is a position and ball is a prefab I created, but unfortunately this prefab has a Position animation – jumping ball – and because of that as it animates it stays in animation’s position. I can’t even Translate it.
How can I move it or change animation somehow ?

There is more than one way to solve this problem, depending on your other goals/constraints if any.
One simple approach is to separate this problem into two spaces, via the introduction of an empty parent node.
If you construct..
..then you can still apply the animation to [Ball], now within a “local space” defined by [Empty Parent Node]. Further, you can now specify an arbitrary position for the parent node, which acts to place the ball overall.