In this lecture on Frobenius endomorphisms, we imagine a Galois extension over $\mathbb{Q}$ given as $M=\mathbb{Q}/(f(x))$ for an irreducible monic polynomial $f(x)\in\mathbb{Z}[x]$. We then consider $R = \mathbb{Z}[x]/(f(x))$ and $R/pR$. If $f(x)=f_1(x)\dots f_k(x)\in (\mathbb{Z}/p\mathbb{Z})[x]$, then $R/pR$ splits into a product of fields $F_i: = (\mathbb{Z}/p\mathbb{Z})[x]/(f_i(x))$.
Any automorphism of $R$ will give an automorphism of $R/pR$, and this will permute the roots of $f(x)$. This will either permute the fields $F_i$ in the decomposition of $R/pR$, or permute the roots within each field.
The claim he makes that confuses me (at around 9:27) is that if an automorphism maps $F_1$ to itself, then this automorphism is the identity on $R$ if and only if it induces the identity on $F_1$. I can see that a non-identity automorphism on $R$ must give a non-identity automorphism on $R/pR$, but I don't see why I couldn't have an automorphism that acts as the identity on $F_1$, but has a non-trivial action on some other field $F_i$ in the decomposition of $R/pR$.
As an example, suppose I have a polynomial $f(x)$ over the rationals that has real and complex roots. If $f(x)=f_1(x)f_2(x)\mod p$, and all the real roots end up as roots of $f_1(x)$, then complex conjugation would be the identity on $F_1$ but not the identity on $F_2$. So this can't happen?