Traditionally, by indicated an agent, the doer of the action, and with indicated the instrument used by the agent.
However, there's a large grey area between the two.
If a fan hit Andrew with a stone, the implication is that the fan was holding the stone and using it as a weapon.
If Andrew was hit by a stone, the implication is that the fan threw the stone at Andrew or, in other circumstances, that the stone was dislodged and fell on Andrew.
The same applies to plastic bottles. One can be struck with a plastic bottle or by a plastic bottle.
When it comes to missiles, it's more complicated. People are struck by bullets and arrows, even though these are instruments rather than agents. You can also be struck by a (flying) knife although you are more likely to be stabbed with one.
We also talk about people being hit by a bus and killed by falling trees. You might be killed with a tree, but only if somebody was using the tree to kill you, which is a bit improbable although not impossible.
So the choice of preposition depends on the context and on idiomatic use.