In characteristics two and three you don't have the short Weierstrass form, and this leaves room for more examples. Below there are examples of
- $q=2$, $r=2$,
- $q=2$, $r=3$,
- $q=4$, $r=2$.
Consider the elliptic curve
$$
y^2+y=x^3+x
$$
defined over $\Bbb{F}_2$. It is relatively easy to see that all the solutions with
$x,y\in\Bbb{F}_4$ actually have $x,y\in\Bbb{F}_2$. Basically because $y^2+y=0$ when $y\in \Bbb{F}_2$, and $y^2+y=1$ when $y\in\Bbb{F}_4\setminus \Bbb{F}_2$,
but $x^3+x\neq0,1$ when $x\in\Bbb{F}_4\setminus\Bbb{F}_2$.
An explanation in terms of Hasse-Weil formula is to observe that $\# E(\Bbb{F}_2)=5$,
Every point $(x,y)\in\Bbb{F}_2\times\Bbb{F}_2$ is a solution, and then we have the point at infinity. Therefore
$$
\alpha+\overline{\alpha}=\alpha+\frac2\alpha=-2.
$$
Squaring this equation gives
$$
\alpha^2+\overline{\alpha^2}=\alpha^2+\frac4{\alpha^2}=(\alpha+\frac2\alpha)^2-4=(-2)^2-4=0.
$$
Therefore $\# E(\Bbb{F}_4)=4+1-0=5=\# E(\Bbb{F}_2).$
Other characteristic two examples are the curves
$$
y^2+xy=x^3+1
$$
and
$$
y^2+xy=x^3+x.
$$
Both have four points over $\Bbb{F}_2$ but no other solutions over $\Bbb{F}_8$.
From $\#E(\Bbb{F}_2)=4$ we can solve $\alpha=(-1+i\sqrt7)/2$. Then
$\alpha^3=(5-i\sqrt7)/2$ and thus, by Hasse-Weil
$$
\# E(\Bbb{F}_8)=8+1-(\alpha^3+\overline{\alpha^3})=8+1-5=4.
$$
An alternative explanation comes from the fact that the trace of $(x+\dfrac1x)$ is equal to
$1$ for all $x\in\Bbb{F}_8\setminus\Bbb{F}_2$. The solvability criterion for
having a solution $y\in\Bbb{F}_8$ would dictate this trace to vanish. Hence, no new points.
Yet another characteristic two example.
Consider the curve $$y^2+y=x^3.$$ With $x$ ranging over the field $\Bbb{F}_4$ we have $x^3\in\Bbb{F}_2$, therefore two solutions for $y$ to each $x$ and therefore nine points altogether. In this maximal case we must have $\alpha=\overline{\alpha}=-2$. But, then $\alpha^2=\overline{\alpha}^2=4$, so over the field $\Bbb{F}_{16}$ we have $16+1-(\alpha^2+\overline{\alpha}^2)=9$ points also. The trace condition for solvability of a quadratic leads to the same conclusion. After all, the cube of an element $x\in\Bbb{F}_{16}\setminus\Bbb{F}_4$ is of order five, and those all have trace $1$.