Find the Jordan decomposition of $$ A := \begin{pmatrix} 4 & 0 & 1 \\ 0 & 1 & 0 \\ 1 & 0 & 3 \end{pmatrix} \in M_3(\mathbb{F}_5), $$ where $\mathbb{F}_5$ is the field modulo 5.
What I've done so far The characteristic polynomial is \begin{equation} P_A(t) = (4 - t)(1-t)(3-t) - (1-t) = -t^3 + 8t^2-18t+1 \equiv 4t^3 + 3t^2 + 2t + 1 \mod5. \end{equation} Therefore, $\lambda = 1$ is a zero of $P_A$, since $4+3+2+1 = 10 \equiv 0 \mod 5$. By polynomial division one obtains $$ P_A(t) = (t + 4)(4t^2 + 2t + 4) = (t + 4)(t + 4) (4t + 1) \equiv 4 (t + 4)^3 $$ Therefore $\lambda = 1$ is the only eigenvalue of $A$. To find the eigenspace we calculate the kernel of $A + 4 E_3$ and obtain $$ \text{span}\left( \begin{pmatrix} 1 \\ 0 \\ 2 \end{pmatrix}, \begin{pmatrix} 1 \\ 1 \\ 2 \end{pmatrix} \right) $$ Since $(A + 4 E_3)^2 = 0$, the kernel of $(A + 4 E_3)^2$ is the whole space. Now, I choose $v := (1, 0, 0) \in \text{ker}(A + 4 E_3)^2$ such that $v \not\in \text{ker}(A + 4 E_3)$. We calculate $(A + 4E)v = (3, 0, 1)$ and then $$ (A + 4E) \begin{pmatrix} 3 \\ 0 \\ 1\end{pmatrix} = \begin{pmatrix} 0 \\ 0 \\ 0 \end{pmatrix}, $$ but the zero vector can't be a basis vector of our Jordan decomposition.
Have I made a mistake in my calculations?
Your calculations are fine. However, by definition of kernels, an element of the kernel of $(A+4E)^2$ vanishes when applying $A+4E$ to it twice, so you should not be surprised. You just made the wrong conclusion. The eigenvector $(3,0,1)$ together with the generalized eigenvector $(1,0,0)$ form part of a Jordan basis giving you a Jordan block of size $2$. All you need to do is add another eigenvector which is linear independent to $(3,0,1)$, for example $(1,1,2)$.
Then $$ \begin{pmatrix} 3 & 1 & 1 \\ 0 & 0 & 1 \\ 1 & 0 & 2 \end{pmatrix}^{-1} \begin{pmatrix} 4 & 0 & 1 \\ 0 & 1 & 0 \\ 1 & 0 & 3 \end{pmatrix} \begin{pmatrix} 3 & 1 & 1 \\ 0 & 0 & 1 \\ 1 & 0 & 2 \end{pmatrix} = \begin{pmatrix} 1 & 1 & 0 \\ 0 & 1 & 0 \\ 0 & 0 & 1 \end{pmatrix}. $$