Problem: let $\zeta$ be a primitive $9$th root of unity, and $K = \mathbb{Q}(\zeta)$. Describe the lattice of subfields of $K$, give generators for each subfield and list its degree over $\mathbb{Q}$.
Okay, so $K/ \mathbb{Q}$ is Galois with group $G \cong U(\mathbb{Z}/9\mathbb{Z}) \cong \mathbb{Z}/6 \mathbb{Z}$, generated by the map $\phi$ given by $\phi(\zeta) = \zeta^2$. So $G = \{\phi, \phi^2, \phi^3, \phi^4 , \phi^5, 1\}$ and the nontrivial proper subgroups are $H_1 = \{\phi^2, \phi^4, 1\}$ and $H_2 = \{ \phi^3, 1\}$.
As for the fixed field $F_2$ of $H_2$, we have $\phi^3(\zeta^j) = \phi^3(\zeta)^j = \zeta^{8j}$ for any $j$. I take the basis $1, \zeta, ... , \zeta^5$ of $K/ \mathbb{Q}$ and look for all elements $\alpha = a_0 + a_1 \zeta + \cdots + a_5 \zeta^5$ which are equal to $a_0 + a_1 \zeta^8 + a_2 \zeta^{16} + a_3 \zeta^{24} + a_4 \zeta^{32} + a_5 \zeta^{40}$. The minimal polynomial of $\zeta$ is $X^6 + X^3 + 1$, so $\zeta^6 = - \zeta^3 - 1; \zeta^7 = - \zeta^4 - \zeta;$ and $\zeta^8 = \zeta^5 - \zeta^2$. Also $\zeta^{16} = \zeta^7, \zeta^{24} = \zeta^6$, $\zeta^{32} = \zeta^5$, and $\zeta^{40} = \zeta^4$.
Thus $$a_0 + a_1 \zeta^8 + a_2 \zeta^{16} + a_3 \zeta^{24} + a_4 \zeta^{32} + a_5 \zeta^{40} $$ $$ = a_0 + a_1(\zeta^5 - \zeta^2) + a_2(-\zeta^4 - \zeta) + a_3(-\zeta^3 - 1) + a_4\zeta^5 + a_5 \zeta^4 $$$$ = (a_0 - a_3) - a_2 \zeta - a_1 \zeta^2 - a_3 \zeta^3 + (-a_2 + a_5) \zeta^4 + (a_1 +a_4) \zeta^5$$
So to have $\alpha \in F_2$, we need $a_0 = a_0 - a_3$ (which implies $a_3= 0$), $a_1 = -a_2, a_2 = -a_1$ (that's redundant but oh well), $a_3 = -a_3$ (i.e. $a_3 = 0$ again redundant). We also need $a_4 = -a_2 + a_5$ (or $a_4 = a_1 + a_5$) and $a_1 + a_4 = a_5$. Thus $a_4 = a_1 + a_1 + a_4 = 2a_1 + a_4$, or $a_1 = 0$ and $a_4 = a_5$. Thus also $a_2 = 0$.
Thus $F_2 = \{ a_0 + a_4 (\zeta^4 + \zeta^5) : a_0, a_4 \in \mathbb{Q} \}$
So $F_2 = \mathbb{Q}[\zeta^4 + \zeta^5]$. Also $[F_2 : \mathbb{Q}] = |Aut(F_2/ \mathbb{Q})| = |Aut(K/ \mathbb{Q})/ Aut(K/F_2)| = 6/2 = 3$.
As for $F_1$, the fixed field of $H_1 = \{\phi^2, \phi^4, 1\}$, it necessarily has degree $6/3 = 2$ over $\mathbb{Q}$. But I already know such a subfield. $\zeta^3$ is a primitive $3rd$ root of unity, and $\mathbb{Q}[\zeta^3]$ is a subfield of $K$ with degree $\phi(3) = 2$ over $\mathbb{Q}$, so it is the desired result.
Was my field $F_1$ correct? Is there a faster way to find it?
$F_1$ is correct, and your method seems direct enough. However, you might better recognize $F_2$ as the maximal real subfield of $K$, i.e. $\mathbb{Q}(\zeta+\zeta^{-1})$. Your expression for $F_2$ seems incorrect. I hesitate to say where you went wrong.