There are many ways to derive the Black Scholes PDE. The Martingale way would be to demand the option price is driftless according to particular measures. Below I derive the correct PDE using the bank account as the numeraire but fail to get the correct PDE when using the stock as a numeraire. I am hoping someone will be able to point out what I am doing wrong.
Deriving Black Scholes PDE using bank account as numeraire
One of the ways to derive the Black-Scholes equation is to take the bank account $B_t$ as a numeraire and then demand that $d\frac{C_t}{B_t}$ be driftless. Below I keep the subscript denoting time implicit.
Concretely, under this numeraire $W_B$ (where $B$ stands for bank account)
$$ dS=S r dt + S \sigma dW_B \\ dB=B r dt $$ so we simply get $$ \begin{eqnarray} d\frac{C}{B} &=& \frac{\partial_t C dt + \partial_S CdS + \frac{1}{2} \partial_{S,S} CdS^2 }{B}-\frac{CdB}{B^2} \\ &=& \frac{\partial_t C + r S\partial_S C + \frac{1}{2} \sigma^2 S^2\partial_{S,S} C -rC}{B} dt + \frac{\sigma S \partial_S C}{B} dW_B + \mathcal O({dt}^{3/2}) \end{eqnarray} $$ and demanding that $\frac{C}{B}$ be a Martingale requires the vanishing of the drift term and we get the Black Scholes PDE: $$ \partial_t C + r S\partial_S C + \frac{1}{2} \sigma^2 S^2\partial_{S,S} C -rC=0 $$
Trying to derive Black Scholes PDE using stock as numeraire
Now I try to do the same while taking the Stock as a numeraire. I will demand, as usual, that $d \frac{C}{S}$ is a Martingale under this measure. Under this measure we have $$ dS = S(r+\sigma^2) dt + S \sigma dW_S $$ so we get $$ \begin{eqnarray} d\frac{C}{S} &=& \frac{\partial_t C dt + \partial_S CdS + \frac{1}{2} \partial_{S,S} CdS^2 }{S}-\frac{CdS}{S^2} + \frac{CdS^2}{S^3} \\ &=& \frac{\partial_t C + (r+\sigma^2) S\partial_S C + \frac{1}{2} \sigma^2 S^2\partial_{S,S} C}{S} dt + \frac{\sigma S\partial_S C dW_S}{S} - \frac{C}{S}\big((r+\sigma^2) dt + \sigma dW_S \big)+\frac{C}{S}\sigma^2 dt +\mathcal O(dt^{3/2}) \\ &=& \frac{\partial_t C + (r+\sigma^2) S\partial_S C + \frac{1}{2} \sigma^2 S^2\partial_{S,S} C -rC}{S} dt + \frac{\sigma S \partial_S C-C}{S} dW_S +\mathcal O({dt}^{3/2}) \end{eqnarray} $$
NOW demanding the drift term to be zero gives me an extra term $$ \partial_t C + (r+\color{red}{\sigma^2}) S\partial_S C + \frac{1}{2} \sigma^2 S^2\partial_{S,S} C -rC=0 $$