Edit: In my original post I failed to require the group to be a manifold group. The answer below from @BenLinowitz works in that case. I am really interested though in when the group is torsion-free, so have edited this to reflect that.
For a non-elementary finite-covolume Kleinian group $\Gamma$, let $\mathbb{Q}(\mathrm{tr}\Gamma)$ and $k\Gamma$ be the trace field and the invariant trace field of $\Gamma$, in the sense of Maclachlan-Reid and Neumann-Reid.
If $\Gamma$ is derived from a quaternion algebra, then $\mathbb{Q}(\mathrm{tr}\Gamma)=k\Gamma$. What I want to know is, what is an example of a case where $\Gamma$ is arithmetic and torsion-free (but not derived from a quaternion algebra, of course), and $\mathbb{Q}(\mathrm{tr}\Gamma)\neq k\Gamma$?
Definitions:
The trace field of $\Gamma$ is $\mathbb{Q}(\mathrm{tr}\Gamma):=\mathbb{Q}\big(\{\mathrm{tr}\gamma\mid\gamma\in\Gamma\}\big)$.
The invariant trace field of $\Gamma$ is $k\Gamma:=\mathbb{Q}(\mathrm{tr}\Gamma^{(2)})$, where $\Gamma^{(2)}:=\langle\gamma^2\mid\gamma\in\Gamma\rangle$ (the group generated by squares in $\Gamma$).
$\Gamma$ is derived from a quaternion algebra if there exists a quaternion algebra $B$ that has a unique complex place, and is ramified at all real places, and an order $\mathcal{O}\subset B$ so that $\Gamma$ is a finite-index subgroup of $\mathrm{P}\mathcal{O}^1:=\{x\in\mathcal{O}\mid\mathrm{nrd}(x)=1\}/\{\pm1\}$.
$\Gamma$ is arithmetic if it is commensurable to a group derived from a quaternion algebra.
Properties:
$\mathbb{Q}(\mathrm{tr}\Gamma)$ and $k\Gamma$ are number fields.
If $\Gamma$ and $\Gamma'$ are commensurable (up to conjugation), then $k\Gamma=k\Gamma'$.
The definition given of arithmeticity is equivalent to $\Gamma$ being Kleinian and and an arithmetic group in the sense of Borel (the ramification conditions guarantee discreteness).