The difference between kinematics and dynamics that Grisha pointed to in his answer comes up in a similar but slightly more complicated case:
Consider (in 1D) two point-like particles connected by a spring ("the molecule"), the right of them being hit by a third particle ("the bullet") coming from the right with initial velocity $v_0$. Let the molecule be in rest initially. Let all three particles have equal mass $m$.
After the collision took place the bullet will move to the right with velocity $v_b$, the molecule will move to the left with velocity $v_m$ and oscillate with frequency $\omega$ and amplitude $\alpha$.
The total energy of the molecule and its total momentum after the collision are then (I hope I didn't make any serious errors):
$E = \frac{m}{2}(v_1^2 + v_2^2) = m (v_m^2 + \alpha^2\omega^2)$
$p = 2mv_m$
The conservation laws yield:
$v_m = \frac{1}{3}(v_0 + \sqrt{v_0^2 - 3\alpha^2\omega^2})$
$v_b = v_0 - 2v_m$
Since we know that $v_m \geq \frac{1}{2}v_0$ we get
$0 \leq \alpha \leq \frac{v_0}{2\omega}$
I.e., the range in which the amplitude $\alpha$ can vary depends on the spring constant $k$ (which is associated with the frequency by $\omega \propto \sqrt{k/m}$): if the spring constant tends to $\infty$ the amplitude must tend to 0 and the molecule must behave approximately like a rigid rod of mass $2m$, as would have been expected.
In any case, the amplitude $\alpha$ is not determined by the conservation laws, only its range of possible values. (This is analoguous to the case of two colliding point-like particles, see answers to Where do particles go after collision?)
But: At least I would see it as unphysical if the molecule would not oscillate after the collision for finite spring constants $k>0$, which is nevertheless allowed by the conservation laws. I cannot imagine an "inner structure" or a micro-process taking place during the collision which would produce this behaviour. What results could inverse scattering experiments yield?
How am I to think about this mind-boggling puzzle?
[Postscript] In the case of two colliding point-like particles it is easy to specify the dynamics in a most natural way, at least in the case when the two collide with diametrical velocities: "for symmetry reasons" their velocities after the collision shall be in the same/opposite direction. (For real point-like particles without inner structure that's the only law/rule that makes sense.)
But now the puzzle continues: Which "natural" law could determine the solution of the molecule-bullet-problem?
