Mirror modifier is not used the way you want to use it here, it's generally used to symmetrize a topology, not to duplicate an object in a scene. Also the Mirror modifier will use the origin of the object as center of the symmetry, so if you wanted to create a symmetrical tree you needed to move the mesh away from the origin (or move the origin).
Also, do you have a reason why you don't join the trunk to the leaves CtrlJ? As Christopher says it would make sense to have only one object.
Instead of using the Mirror modifier you could link duplicate the object with AltD then press SX-1 or SY-1 and you'll have a mirrored version of your object and the meshes are still linked.
You can also use Collection Instances instead of Linked Duplications, see here.
Also some rotations on Z and you won't realise that it's the same tree.