I have been searching google about the gradient of a vector. I have found two distinct types of matrix notation for the gradient of a vector. I can't understand which one is correct, or if both are correct. The two are:
$$\nabla A = \partial_iA_je_i\otimes e_j=\begin{bmatrix}\frac{\partial A_1}{\partial X_1} &\frac{\partial A_2}{\partial X_1} & \frac{\partial A_3}{\partial X_1}\\\frac{\partial A_1}{\partial X_2} & \frac{\partial A_2}{\partial X_2} & \frac{\partial A_3}{\partial X_2}\\\frac{\partial A_1}{\partial X_3} & \frac{\partial A_2}{\partial X_3} & \frac{\partial A_3}{\partial X_3}\end{bmatrix}$$
or the transpose of the first, that is
$$\nabla A = \begin{bmatrix}\frac{\partial A_1}{\partial X_1} & \frac{\partial A_1}{\partial X_2} & \frac{\partial A_1}{\partial X_3}\\\frac{\partial A_2}{\partial X_1} & \frac{\partial A_2}{\partial X_2} & \frac{\partial A_2}{\partial X_3}\\\frac{\partial A_3}{\partial X_1}& \frac{\partial A_3}{\partial X_2}& \frac{\partial A_3}{\partial X_3}\end{bmatrix}.$$
The gradient of a function is well defined in the literature. The gradient of a vector field $A = A^i\partial_i$ seems to be the gradient of its components (which are functions). I think both matrix representations ($\partial_i A^j$ and $\partial_j A^i$) are "good" since they are simply representations of the same thing : $$\nabla A = (\partial_i A^j)dx^i\otimes \partial_j = (\partial_j A^i)dx^j \otimes \partial_i$$ Choose one of them and stay with it (at least until the end of the proof where you are using gradients of vector field).
Geometrically speaking, the gradient of a vector field you are talking about can be written either as the Lie derivative $\mathcal{L} A$ (along $\partial_i$ or $\partial_j$) or the covariant derivative $\nabla A$ (with vanishing Christoffel symbols $\Gamma$'s) (along $\partial_i$ or $\partial_j$). Both $\mathcal{L} A$ and $\nabla A$ are a little bit overkill for your setting (probably Euclidean flat space) but are good to keep in mind if you need to generalize from $\mathbb{R}^n$ to some manifold with global properties.