The example I am using is polar coordinates, however my confusion can be extended.
so we have $f(x,y)$ where $x = x(r,\theta)$ and $y = y(r,\theta) $
The first derivative I understand:
$$\left(\frac{\partial f}{\partial x}\right)_y=\left(\frac{\partial f}{\partial r}\right)_\theta\left(\frac{\partial r}{\partial x}\right)_y+\left(\frac{\partial f}{\partial \theta}\right)_r\left(\frac{\partial \theta}{\partial x}\right)_y$$
now if we differentiate with respect to x again - I have used the product rule on both functions in each term:
$$\left(\frac{\partial^2 f}{\partial x^2}\right)_y= \left(\frac{\partial^2 f}{\partial r^2}\right)_\theta\left(\frac{\partial r}{\partial x}\right)_y^2 + \left(\frac{\partial f}{\partial r}\right)_\theta\left(\frac{\partial^2 r}{\partial x^2}\right)_y+ \left(\frac{\partial^2 f}{\partial \theta^2}\right)_r\left(\frac{\partial \theta}{\partial x}\right)_y^2 + \left(\frac{\partial f}{\partial \theta}\right)_r\left(\frac{\partial^2 \theta}{\partial x^2}\right)_y +$$
$$ +2\left(\frac{\partial^2 f}{\partial r \partial \theta}\right)_{\theta r}\,\left(\frac{\partial r}{\partial x}\right)_y \,\left(\frac{\partial \theta}{\partial x}\right)_y $$
However, I believe this to be wrong as we can take
$$\left(\frac{\partial }{\partial x}\right)_y=\left(\frac{\partial }{\partial r}\right)_\theta\left(\frac{\partial r}{\partial x}\right)_y+\left(\frac{\partial }{\partial \theta}\right)_r\left(\frac{\partial \theta}{\partial x}\right)_y$$
Applying this to $(\frac{\partial f}{\partial x})_y$ we get:
$$(\frac{\partial^2 f}{\partial x^2})_y= (\frac{\partial^2 f}{\partial r^2})_\theta(\frac{\partial r}{\partial x})_y^2 + (\frac{\partial^2 f}{\partial \theta^2})_r(\frac{\partial \theta}{\partial x})_y^2 + 2(\frac{\partial^2 f}{\partial r \partial \theta})_{\theta r}(\frac{\partial r}{\partial x})_y (\frac{\partial \theta}{\partial x})_y $$
Where did the
$$ (\frac{\partial f}{\partial r})_\theta(\frac{\partial^2 r}{\partial x^2})_y\;\;,\;\;\;\; (\frac{\partial f}{\partial \theta})_r(\frac{\partial^2 \theta}{\partial x^2})_y$$
terms go? Its as if the product rule doesn't hold, the $\; (\frac{\partial r}{\partial x})_y\;\;,\;\;\; (\frac{\partial \theta}{\partial x})_y\;$ didn't get differentiated.
Where is my mistake? thank you