Firstly, I think that some terminology may be causing some problems. The Frobenius automorphism in a field of characteristic $p$ is the map $x\mapsto x^p$ and respects all of the field operations and fixes elements of the subfield $\mathbb F_p$ and other subfields are closed under the map. The Frobenius endomorphism of an elliptic curve over a field of characteristic $p$ is the map generated by applying the Frobenius automorphism co-ordinatewise: $\phi:(x,y)\mapsto (x^p,y^p)$. As the elliptic curve group law only uses field operations of coordinates and curve coefficients, $\phi$ respects both point addition: $\phi((x_1,y_1)+(x_2,y_2))=\phi(x_1,y_1)+\phi(x_2,y_2)$ and scalar multiplication: $\phi(k(x,y))=k\phi(x,y)$. The map fixes points of $E(\mathbb F_p)$ and the groups of points over other subfields are closed under the map if the curve coefficients lie in $\mathbb F_p$.
If we consider the full $q$-torsion subgroup this is defined as the set of points where $\{P:qP=\mathcal O\}$ and since $q\phi(P)=\phi(qP)$ the subgroup is closed under the Frobenius endomorphism. Similarly, it is easy to see that elements of the intersection of this subgroup with $E(\mathbb F_p)$ are fixed. However, it is not true that other subgroups are closed under this map. A numerical example might help at this point if you are familiar with sagemath. Let's take a simple example of a supersingular curve with coefficients in $GF(283)$ this has 284 points over $GF(283)$ and has a subgroup of order 71 over the base field. Over $GF(283^2)$, there are $284^2$ points and the full 71-torsion subgroup of $71^2$ points is realised. We can decompose this into a product of $H_1$ the $E(GF(283))$ subgroup and $H_2$ where $H_2$ any subgroup generated by a $q$-torsion point that does not lie in $E(GF(283))$. Note that $\# H_1=71$ and $\# H_2=71$ so that there are points of the torsion group that lie in neither $H_1$ nor $H_2$. We can find generators for $H_1$ and an arbitrary choice of $H_2$ with high probability by taking random points of $E(GF(283))$ and $E(GF(283^2)$ respectively and scalar multiplying by 4 (which is the cofactor in this case).
sage: q=71
sage: p=283
sage: E1=EllipticCurve(GF(p),[-1,0])
sage: E1.count_points()
284
sage: E2=EllipticCurve(GF(p^2),[-1,0])
sage: E2.count_points()
80656
sage: P=E2(4*E1.random_point())
sage: P
(265 : 176 : 1)
sage: Q=4*E2.random_point()
sage: Q
(136*z2 + 63 : 148*z2 + 187 : 1)
sage: q*P
(0 : 1 : 0)
sage: q*Q
(0 : 1 : 0)
Now consider applying the Frobenius map to $Q$ to produce a point $R$, we get a point that is in the full torsion subgroup, but is not the subgroup generated by $Q$:
sage: R=E2(Q[0]^p,Q[1]^p)
sage: R
(147*z2 + 199 : 135*z2 + 52 : 1)
sage: q*R
(0 : 1 : 0)
sage: for k in range(q):
....: if(k*Q==R):
....: print(k)
....:
sage:
In particular, $R$ is not $pQ$ and $H_2=\langle Q\rangle$ is not closed under Frobenius.