Perfect squares representing the number of rational points on elliptic curves over finite field extensions

Let q be a perfect power of a prime number p and $E({\mathbb{F}}_q)$ be an elliptic curve over ${\mathbb{F}}_q$ given by the equation $y^2=x^3+Ax+B$. For a positive integer n we denote by $\mathrm{\#}E({\mathbb{F}}_{q^n})$ the number of rational points on E (including infinity) over the extension ${\mathbb{F}}_{q^n}$. Under a mild technical condition, we show that the sequence ${\{\mathrm{\#}E({\mathbb{F}}_{q^n})\}}_{n>0}$ contains at most 10²⁰⁰ perfect squares. If the mild condition is not satisfied, then $\mathrm{\#}E({\mathbb{F}}_{q^n})$ is a perfect square for infinitely many n including all the multiples of 12. Our proof uses a quantitative version of the Subspace Theorem. We also find all the perfect squares for all such sequences in the range $q<50$ and $n\le 1000$.