For the matrix
$$A=\begin{pmatrix} 0 & 1 & 0 \\ 0 & 0 & 1 \\ 1 & 0 & 0 \end{pmatrix}$$
an annihilating polynomial is $x^3-1$, but its characteristic polynomial is $x^3+1$.
Is this a contradiction, since roots of characteristics polynomial should be roots of annihilating polynomial too?
You just made a mistake calculating the characteristic polynomial. The characteristic polynomial is $-x^3 + 1$, which is just your annihilating polynomial times $-1$.