Given is the curve $\mathbf{\gamma}(p)$ with components
$x(p)=\sin(p)$
$y(p)=\cos(p)$
$z(p)=p$
Then $\frac{d\mathbf{\gamma}(p)}{dp}=\left(\begin{array}{c} \cos(p)\\ -\sin(p)\\ 1\\ \end{array}\right)$
Let $\mathbf{A}(p)=\frac{d\mathbf{\gamma}(p)}{dp}$. Expressing $\mathbf{A}(p)$ via the coordinates we can write
$\mathbf{A}(p)(1)=\left(\begin{array}{c} y(p)\\ -\sqrt{1-y^2(p)}\\ 1\\ \end{array}\right)$, or
$\mathbf{A}(p)(2)=\left(\begin{array}{c} \sqrt{1-x^2(p)}\\ -x(p)\\ 1\\ \end{array}\right)$, or
$\mathbf{A}(p)(3)=\left(\begin{array}{c} y(p)\\ -x(p)\\ 1\\ \end{array}\right)$, or
$\mathbf{A}(p)(4)=\left(\begin{array}{c} \cos(z(p))\\ -\sin(z(p))\\ 1\\ \end{array}\right)$.
They are different ways to write A. Now, write the chain rule
$\frac{d\mathbf{A}(p)}{dp}=\frac{\partial \mathbf{A}}{\partial x} \frac{dx}{dp}+\frac{\partial \mathbf{A}}{\partial y} \frac{dy}{dp}+\frac{\partial \mathbf{A}}{\partial z} \frac{dz}{dp}$
Plug in $\mathbf{A}(p)(1)$ and get
$\frac{d\mathbf{A}(p)}{dp}(1)=\left(\begin{array}{c} -\sin(p)\\ \frac{-y \sin(p)}{\sqrt{1-y^2}}\\ 0\\ \end{array}\right)=\left(\begin{array}{c} -\sin(p)\\ -\cos(p)\\ 0\\ \end{array}\right)$
Plug in $\mathbf{A}(p)(2)$ and get
$\frac{d\mathbf{A}(p)}{dp}(2)= \left(\begin{array}{c} \frac{-x \cos(p)}{\sqrt{1-x^2}}\\ -\cos(p)\\ 0\\ \end{array}\right)=\left(\begin{array}{c} -\sin(p)\\ -\cos(p)\\ 0\\ \end{array}\right)$
Plug in $\mathbf{A}(p)(3)$ and get
$\frac{d\mathbf{A}(p)}{dp}(3)= \left(\begin{array}{c} 0\\ -1\\ 0\\ \end{array}\right)\cos(p)+\left(\begin{array}{c} 1\\ 0\\ 0\\ \end{array}\right)(-\sin(p))+0=\left(\begin{array}{c} -\sin(p)\\ -\cos(p)\\ 0\\ \end{array}\right)$
Plug in $\mathbf{A}(p)(4)$ and get
$\frac{d\mathbf{A}(p)}{dp}(4)=0+0+ \left(\begin{array}{c} -\sin(z)\\ -\cos(z)\\ 0\\ \end{array}\right)=\left(\begin{array}{c} -\sin(p)\\ -\cos(p)\\ 0\\ \end{array}\right)$
In all cases the result ends up the same, but the partial derivatives $\frac{\partial\mathbf{A}}{\partial x_i}$ are ambiguous. Still, adding ambiguous terms together consistently results in a correct answer.
User Med suggested that since $y(p)$ is not independent of $x(p)$ etc., we can apply the following chain rule to remove ambiguity:
$\frac{\partial \mathbf{A}}{\partial x_i}= \frac{d\mathbf{A}}{dp}\frac{dp}{dx_i} = \frac{d\mathbf{A}}{dp}\frac{1}{\frac{dx_i}{dp}}$, which works fine in cases (1), (2) and (4), because $\mathbf{A}$ contains only one space variable.
But is case (3) both partial derivatives w/respect to x and y are nonzero and then this workaround can't be used anymore.
Is there a general approach how to avoid the ambiguity in the partial derivatives? How do I express $\frac{\partial\mathbf{A}}{\partial x_i}$ in case (3)?
I think you're getting tripped up by the notation, which can easily happen when using the derivative notation $\partial \mathbf A/\partial x$. $\newcommand{\A}{\mathbf A}$
The chain rule says that if $\A(x,y,z)$ is a multivariable function, and then we construct the single-variable function $\A\big(x(p),\ y(p),\ z(p) \big)$ with $x$, $y$, and $z$ functions of another variable $p$, then the derivative of the single-variable function of $p$ is $$ \frac{d}{dp} \A\big(x(p),\ y(p),\ z(p) \big) = \frac{\partial \A}{\partial x} \frac{dx}{dp}\ +\ \frac{\partial \A}{\partial y} \frac{dy}{dp}\ +\ \frac{\partial \A}{\partial z} \frac{dz}{dp} $$ where the notation $\partial \A/\partial x$ in this context denotes the partial derivative of the multivariable function $\A$ with respect to its first component evaluated at the particular vector $\big(x(p), y(p), z(p) \big)$ for every $p$, and similarly for $\partial \A/\partial y$ and $\partial \A/\partial z$.
The critical thing to note is that $\A$ denotes a multivariable function that takes any triple $(x,y,z)$ and maps it to another triple. But $\A\big(x(p),\ y(p),\ z(p) \big)$ denotes the single-variable function that takes a number $p$ and returns a triple. In other words, it is a composition of a multivariable function with a single-variable function, thus resulting in a single-variable function. That means the notation $\frac{\partial}{\partial x} \A\big(x(p),\ y(p),\ z(p) \big)$ is meaningless: how can we take the partial derivative of a single-variable function?
The difference for your case is that you defined (before you ever mentioned the chain rule) that $\A(p)$ equals something. That makes $\A$ a single-variable function. Thus (strictly speaking) the expression $\partial \A/\partial x$ is meaningless. Although you note that $\A$ can be rewritten so that it looks like a multivariable function. Here's one rewriting (the one you're chiefly interested in): $$ \mathbf{A}(p)=\left(\begin{array}{c} y(p)\\ -x(p)\\ 1\\ \end{array}\right) $$ Even written like this, $\A$ is still merely a single-variable function. But it fits the template of a multivariable function. Namely this one: $$(x,y,z) \mapsto \begin{pmatrix} y \\ -x \\ 1 \end{pmatrix} $$ $\newcommand{\T}{\mathbf T}$ I'll call this function $\T$ for template. In that case, we may write $$ \A(p) = \T\big(x(p),\ y(p),\ z(p) \big) $$ and write the chain rule as \begin{align} \frac{d\A}{dp} &= \frac{\partial \T}{\partial x} \frac{dx}{dp} + \frac{\partial \T}{\partial y} \frac{dy}{dp} + \frac{\partial \T}{\partial z} \frac{dz}{dp} \\ &= \begin{pmatrix} 0 \\ -1 \\ 0 \end{pmatrix} \cos p + \begin{pmatrix} 1 \\ 0 \\ 0 \end{pmatrix} \cdot -\sin p + \begin{pmatrix} 0 \\ 0 \\ 0 \end{pmatrix} \cdot 1 \\ &= \begin{pmatrix} -\sin p \\ -\cos p \\ 0 \end{pmatrix} \end{align} as expected.
Of course, it is a lot of trouble to separately define $\T$, and it looks more intuitive to just write $\partial \A/\partial x$. That's fine as long as it's clear from context what your template function is, and you know what's really going on under the hood.