There is no contraddiction.
First of all $[\phi(x), \partial_\mu \phi(x)]$ is not defined as the two arguments coincide. What we can do is to define the normal order of it
$$:[\phi(x), \partial_\mu \phi(x)]: = :\phi(x)\partial_\mu \phi(x): - :(\partial_\mu\phi(x)) \phi(x):$$
A direct computation proves that
$$:[\phi(x), \partial_\mu \phi(x)]:=0\:,$$
so no contraddiction arises through this way.
Instead CCR implies
$$[\phi(t_x,\vec{x}), v^\mu\partial_\mu \phi(t_y,\vec{y})]|_{t_x=t_y}= i\hbar v^0I\delta(\vec{x}-\vec{y})\tag{1}$$
where both sides are intepreted as 3D distributions on test functions $f=f(\vec{x})$.
Assuming that $v$ is spacelike,  when you change reference frame in order that the components of $v$ are spatial, you must drop the constraint $t_x=t_y$. So, again, no evident contraddiction takes place.
A deeper analysis should be performed referring to $4D$-distributions.
In that case (see this site) the general form of the commutator -- which is evidently $IO(1,3)_+$ invariant -- is
$$[\phi(x),\phi(y)] =  -\frac{1}{(2\pi)^3}\int_{\mathbb{R}^4}\delta(k_\mu k^\mu + m^2)\:\mbox{sign}(k_0) e^{i k_\mu(x^\mu-y^\mu)} d^4k\:.$$
It easily implies the standard commutation relations (also considering derivatives) when passing to the invariant measure on the mass shell and assuming $t_x=t_y$ in any given Minkowskian reference frame.
In summary, for a spacelike vector $v$ (which has only spatial components in the primed reference frame), both
$$[\phi(t_x,\vec{x}), v^\mu \partial_\mu\phi(t_y,\vec{y})]|_{t_x=t_y} = v^0i\delta(\vec{x}-\vec{y})\quad \mbox{and} \quad [\phi(t'_{x'},\vec{x}'),  \sum_{k=1}^3 v'^k\partial'_k\phi(t'_{y'},\vec{y})]|_{t'_{x'}=t'_{y'}}=0$$
are correct. There is no contraddiction: they refer to different Minkowskian frames.