I was taking the inverse of
$$A=\begin{bmatrix} 2+i &1 \\ 1&-2+i \end{bmatrix}$$
and $\det(A)=-6 $, and cofactor matrix
$$C=\begin{bmatrix} -2+i &-1 \\ -1&2+i \end{bmatrix}$$
such that correct way to do it is
$$A^{-1}=\frac{1}{\det(A)}C^{T}$$
but I'm wondering why we are not taking conjugate transpose of C?
Briefly: "most of the time", the correct analog for extending a matrix expression involving a transpose will be the conjugate-transpose. In the case of the inverse, however, the formula for $A^{-1}$ should be a "nice" (i.e. complex-differentiable) function and so we must use the entry-wise transpose.
In the case of real matrices, the transpose "usually" arises when we consider the relationship of a matrix $A$ to the inner-product $\langle x, y \rangle_{\Bbb R} = y^Tx = x^Ty$. More abstractly, this occurs when we consider how the linear transformation induced by $A$ interacts with the usual (Euclidean) geometry on $\Bbb R^n$. For instance, we have the following definitions and statements involving the transpose of a real matrix.
Definitions:
Theorems:
All of these statements and theorems have analogs when we consider complex matrices over the Hermitian inner product, which is defined by $\langle x,y \rangle = y^*x$. In the complex context, any $A^T$ is replaced with $A^*$, the conjugate-transpose of $A$.
Now, let's consider the entry-wise transpose for complex matrices and the corresponding bilinear form $(x,y) = y^Tx = x^Ty$. Here are some things that go wrong.
There is, however, something gained in this case. Because $(x,y)$ is a polynomial on the entries of $x$ and $y$ (whereas $\langle x, y \rangle$ fails to be complex-differentiable), formulas involving the entry-wise transpose behave nicely with respect to computations involving complex numbers, including complex-differentiation.
For instance: the matrices satisfying $A^T = A$ form a complex subspace of $\Bbb C^{n \times n}.$ Also, the set of complex-orthogonal matrices (i.e. matrices satisfying $A^TA = I$) forms a smooth manifold in $\Bbb C^{n \times n}$.
Another consequence of all this, as you said, is that the correct choice for you determinant formula is the entry-wise transpose rather than the conjugate transpose. In this case, the formula for the cofactor matrix bears no relation to the Euclidean geometry on $\Bbb R^n$ or $\Bbb C^n$.