I know there are similar questions with answers like this one in physics stackexchange but before I read these I had a completely different argument with a different conclusion which I thought was correct but now I'm suspecting that there is something wrong with the argument. I just want to know what exactly is wrong with it.
In a two body problem with say particles of masses $m_1$ and $m_2$ interacting under a central force $f(r)\hat{r}$ where $\mathbf{r} = \mathbf r_2 - \mathbf r_1$ the equations of motion of the two particles are
$$m_1\ddot{\mathbf r}_1 = f(r)\hat{r}$$
$$m_2 \ddot{\mathbf r}_2= -f(r)\hat{r}$$
From these two equations I have $$\ddot{\mathbf{r}}_2 - \ddot{\mathbf{r}}_1 = -f(\mathbf{r}) \hat{r} \left(\frac{1}{m_1} + \frac{1}{m_2} \right)$$ or $$\mu \ddot{\mathbf r} = - f(r)\hat{r}$$ where $\mu = \frac{m_1m_2}{m_1 + m_2}$ Now by just looking at the last equation it seems that there is a single particle under a central force and $\vec{r}$ is just the position vector of that particle.
But I also know that $\vec{r}$ is the separation vector between particles of masses $m_1$ and $m_2$. So it seems to me that when I find the trajectory of $\mu$ (when I find $\vec{r}(t)$) it would also be the trajectory of $m_2$ with $m_1$ at the origin. But it seems my reasoning was wrong because it turns out that the center of mass is at the origin which is further reinforced by the fact that the angular momentum and energy of $\mu$ is the angular momentum and energy of the two body system in the center of mass frame. So there must be something I was missing. But I can't figure out what it is.