I will outline what I believe to a correct way to go from a Lagrangian of a charged particle in a EM field to Lorentz force via the Euler-Lagrange equations. At the very beginning when I use the EL equation, I will bold what my concern is and return to it after I finish the derivation.
The Lagrangian (in SI units) reads
\begin{equation} L = \frac{1}{2} m\dot{r}^2 - q \phi + q \dot{r}\cdot A \end{equation} where both the scalar potential $\phi$ and $A$ depend of space and time $\phi(t,r)$, $A(t,r)$.
Euler Lagrange gives us
\begin{align} \frac{\partial L}{\partial r} - \frac{d}{dt}\frac{\partial L}{\partial \dot{r}} &= 0 \\ -q \frac{\partial }{\partial r} \phi + \mathbf{q \frac{\partial}{\partial r} (\dot{r}\cdot A)} - \frac{d}{dt}(m\dot{r}+\mathbf{qA}) &=0 \\ q\big[-\nabla \phi + \nabla(\dot{r}\cdot A) - \frac{d A}{dt}\big] &= m\ddot{r} \end{align}
then using the following expression for a total time derivative of some function of space and time $f(t,x_1,x_2,...)$,
\begin{align} \frac{d}{dt} f &= \big[\frac{\partial}{\partial t} + \sum \frac{d x_i}{dt} \frac{\partial}{\partial x_i}\big]f \\ &= \big[\frac{\partial}{\partial t} + (\dot{r}\cdot \nabla)\big]f \end{align}
on the $\frac{d A}{dt}$ term we have
\begin{align} q\big[-\nabla \phi + \nabla(\dot{r}\cdot A) - \frac{d A}{dt}\big] &= m\ddot{r} \\ q\big[-\nabla \phi + \nabla(\dot{r}\cdot A) - \frac{\partial A}{\partial t} - (\dot{r}\cdot \nabla) A \big]&= m\ddot{r} \end{align}
then using the ``bac-cab" rule of vector calculus with $\dot{r}=v$ and the magnetic field $B=\nabla\times A$,
\begin{align} a\times b\times c &= b(a\cdot c) - c(a\cdot b) \\ &=b(a\cdot c) - (a\cdot b)c \\ v \times \nabla \times A &= \nabla (v\cdot A) - (v\cdot \nabla)A \\ v \times B &= \nabla (\dot{r} \cdot A) - (\dot{r} \cdot \nabla)A \end{align}
on the $\nabla(\dot{r}\cdot A)$ and $- (\dot{r}\cdot \nabla) A$ terms, we have
\begin{align} q\big[-\nabla \phi + \nabla(\dot{r}\cdot A) - \frac{\partial A}{\partial t} - (\dot{r}\cdot \nabla) A\big] &= m\ddot{r} \\ q\big[-\nabla \phi - \frac{\partial A}{\partial t} + v\times B\big] &= m\ddot{r} \\ \end{align}
which, using $E=-\nabla \phi - \frac{\partial A}{\partial t}$, we have
\begin{align} m\ddot{r} &= q[E+v \times B] \\ F &= q[E+v \times B] \end{align}
Now, why is the $q \frac{\partial}{\partial r} (\dot{r}\cdot A)$ from the $\frac{\partial L}{\partial r}$ term in the EL not simply $\dot{r} \cdot \nabla A$? We take the derivative of the Lagrangian with respect to velocities in the second term, why do we take the partial with respect to r of the velocity in this instance?
If we follow this precedent, why isn't the $\frac{d}{dt}(qA)$ from the from the $\frac{d}{dt}\frac{\partial L}{\partial \dot{r}}$ term in the EL equation $\frac{d}{dt}(\dot{r}\cdot A)$?