Another good example is to take $E=H$ and $F=\Sigma KU$. A key point here is that $KU\wedge H\simeq KU\wedge S\mathbb{Q}$. Indeed, the theory of Landweber exactness says that $\pi_*(KU\wedge H)$ is the universal example of a ring equipped with an isomorphism $f(x)$ from the additive formal group law to the multiplicative formal group law, which gives $\pi_*(KU\wedge H)=\mathbb{Q}[u,u^{-1}]$ with $f(x)=\exp(ux)-1$. From this we get a map $S\mathbb{Q}\to KU\wedge H$, which extends uniquely to a map $KU\wedge S\mathbb{Q}\to KU\wedge H$ of $KU$-modules, and this map is easily seen to be an equivalence. We therefore get
$$ [H,\Sigma KU] = [KU\wedge H,\Sigma KU]^{KU} =
[KU\wedge S\mathbb{Q},\Sigma KU]^{KU} =
[S\mathbb{Q},\Sigma KU].
$$
We can now choose a free resolution $R\to F\to \mathbb{Q}$, giving a cofibration $SR\to SF\to S\mathbb{Q}$. By applying $[-,\Sigma KU]$ to this we get $[S\mathbb{Q},\Sigma KU]=\text{Ext}(\mathbb{Q},\mathbb{Z})$ (which is a rational vector space of uncountable dimension). On the other hand, we have
$$ [H,\Sigma KU\mathbb{Q}]=\text{Hom}(\pi_*(H)\otimes\mathbb{Q},\pi_{*-1}(KU)\otimes\mathbb{Q}) = \text{Hom}(\mathbb{Q},\pi_{-1}(KU)\otimes\mathbb{Q})=0. $$
Here the homotopy groups of $F$ are finitely generated, but the homology groups are not, and $F$ is not connective. For a different kind of example, we could take $E=MU$ and $F=S^1$, so both $E$ and $F$ are $(-1)$-connected and of finite type. Using the Adams spectral sequence, Ravenel proved that $[MU,S/p]_*=0$ for all primes $p$. Using this one can deduce that $[MU\wedge S(\mathbb{Q}/\mathbb{Z}),S]_*=0$, and thus that $[MU,S^1]=[MU\mathbb{Q},S^1]$. Here $MU\mathbb{Q}$ is a wedge of even suspensions of $S\mathbb{Q}$, with $[S^{2n}\mathbb{Q},S^1]=0$ for $n>0$, and $[S\mathbb{Q},S^1]=\text{Ext}(\mathbb{Q},\mathbb{Z})$. It follows that once again we have $[E,F]=\text{Ext}(\mathbb{Q},\mathbb{Z})$ but $[E,F\mathbb{Q}]=0$.