$\newcommand{\Z}{\mathbb{Z}}$ I decided that I would try another way of computing $\pi_4(S_3)$. Take the fibration $S_3 \to K(\Z,3)$ with fiber defined to be $X_4$. I want to directly use this fibration.
From the usual way of computing $\pi_4(S_3)$, I know that $H^4(X_4)=0$ and $H^5(X_4)=\Z/2$. (Briefly, you continue(loop) the above fibration to the left to get the fibration $K(\Z,2) \hookrightarrow X_4 \to S_3$ and then you use that the fundamental class of $K(\Z,2)$ is sent to the fundamental class of $S_3$ by $d_3$ in the cohomology Serre Spectral Sequence. Using leibniz' rule, get that $d_3^{0,4}$ is the multiplication by $2$ map. Since $d_3^{3,2}$ is the zero map, $H^5(X_4)=\Z/2$).
Back to the spectral sequence of the fibration $X_4 \hookrightarrow S_3 \to K(\Z, 3)$
Now I will use that I know the cohomology of all three spaces in the fibration: $H^*(K(\Z,3))=\Z[j]$ where $j$ has degree 3. The only possible differential that could get rid of the $\Z/2=E_2^{0,5}$ is $d_6: \Z/2=E_5^{0,5} \to \Z=E_5^{6,0}$. But $d_6$ must be zero since there are no homomorphisms from $\Z/2 \to \Z$ and $E_2^{0,5}=E_5^{0,5}$ survives to $E_\infty$. Therefore $H^6(S_3) \neq 0$. Contradiction.
What is the flaw in my computation of the spectral sequence of $X_4 \hookrightarrow S_3 \to K(\Z, 3)$?
It is not true that $H^*(K(\mathbb{Z},3))=\mathbb{Z}[j]$ where $j$ is the canonical class in degree $3$. Indeed, since the product must be graded-commutative and $j$ has degree $3$, $j^2=(-1)^{|j||j|}j^2=-j^2$, so $2j^2=0$ (and similarly for all higher powers of $j$). In fact, $j^2\neq 0$ and it generates $H^6(K(\mathbb{Z},3))$, so $H^6(K(\mathbb{Z},3))=\mathbb{Z}/2$, not $\mathbb{Z}$ as you claim, and your differential $d_6$ is nonzero and kills $E^{0,5}_2$.
(In addition to $j^2$ having order $2$, $H^*(K(\mathbb{Z},3))$ also has lots of elements in higher degree which are not in the subring generated by $j$.)