Always good to make a diagram:
$$\begin{matrix}
X & \xrightarrow{\pi_1} & X/H_1 & \xrightarrow{\psi_1} & X/G\\
& & \downarrow\iota & & \downarrow\\
X & \xrightarrow[\pi_2]{} & X/H_2 & \xrightarrow[\psi_2]{} & X/G
\end{matrix}$$
So the task is to show that if there exists a homeomorphism $\iota \colon X/H_1 \to X/H_2$ with $\psi_2 \circ \iota = \psi_1$, then $H_1$ and $H_2$ are conjugate in $G$. (Note: except if $H_1 = H_2$, we do not have $\iota\circ \pi_1 =\pi_2$.)
Now, fix any $\phi_{1} \in H_{1}$. Consider any $x_{0} \in X$ and by normality, we have $\phi_{2} \in H$ such that $\phi_{2}(x_{0}) = \phi_{1}(x_{0})$.
No. The normality of $\pi_i$ says that $H_i$ operates transitively on the fibres of $\pi_i$, not on the fibres of $\pi \colon X \to X/G$. $x_0$ and $\phi_1(x_0)$ generally lie in different orbits under the action of $H_2$, and that means in different fibres of $\pi_2$, i.e. in general, there is no $\phi_2 \in H_2$ with $\phi_2(x_0) = \phi_1(x_0)$. If there always is, then $H_2 \supset H_1$.
So let's prove that if $\iota$ exists, then $H_1$ and $H_2$ are conjugate (the converse holds too, if $H_1$ and $H_2$ are conjugate, then there is such an $\iota$).
Pick any $x \in X$. Choose any $y \in X$ with $\pi_2(y) = \iota(\pi_1(x))$.
Then $\pi_G(y) = \psi_2(\pi_2(y)) = \psi_2(\iota(\pi_1(x))) = \psi_1(\pi_1(x)) = \pi_G(x)$, therefore there is a $g \in G$ such that $gx = y$.
Claim: $\pi_2 \circ g = \iota \circ \pi_1$, i.e. $g$ is a lift of $\iota$.
We know that $\pi_2(gx) = \iota(\pi_1(x))$. Let $z \in X$ arbitrary, and choose a path $\gamma$ connecting $x$ and $z$. Since paths can always be lifted, there is a path $\beta$ in $X$ starting at $y$ such that $\pi_2 \circ \beta = \iota \circ \pi_1 \circ \gamma$. Now,
$$\pi_G \circ \beta = \psi_2\circ \pi_2 \circ \beta = \psi_2 \circ \iota \circ \pi_1 \circ \gamma = \psi_1 \circ \pi_1 \circ \gamma = \pi_G \circ \gamma,$$
that is, $\beta$ is a lift of $\pi_G \circ \gamma$ starting in $y$. But $g\cdot \gamma$ is also such a lift of $\pi_G \circ \gamma$, and hence $\beta = g\cdot\gamma$ by the uniqueness of lifts, and thus $\beta(1) = g\gamma(1) = gz$, whence $\pi_2(gz) = \pi_2(\beta(1)) = \iota(\pi_1(\gamma(1))) = \iota(\pi_1(z))$.
$\pi_2\circ g = \iota \circ \pi_1$ is a different way of writing $H_2g \supset gH_1$ or $gH_1g^{-1} \subset H_2$.
We have not yet used that $\iota$ was supposed to be a homeomorphism, just that it was a continuous map with $\psi_2\circ \iota = \psi_1$. The same construction for $\iota^{-1}$ choosing $y = gx$ and $x$ as starting points shows $\pi_1 \circ g^{-1} = \iota^{-1}\circ \pi_2$ or $g^{-1}H_2 \subset H_1g^{-1}$. Together $H_2 = gH_1g^{-1}$.