You seem to be mixing up a relation, which is a subset $R\subseteq A\times A$, with their elements $(x,y)\in R$. A reflexive relation $R$ has as elements at least all pairs $(x,x)$ for $x\in A$. If $|A|=n$ this means that the $n$ elements $(x,x)$ will be in any reflexive relation. This leaves you with $n^2-n$ other possible elements of $A\times A$ that might or might not be elements of $R$. Hence the number of possible reflexive relations $R$ is $2^{n^2-n}$.
For example when $A=\{1,2,3\}$, every reflexive relation contains the elements $(1,1)$, $(2,2)$ and $(3,3)$, so
$$
R = \{(1,1), (2,2), (3,3), \dots \}.
$$
Now for the remaining $3^2-3 = 6$ elements
$$
(1,2), (1,3), (2,1), (2,3), (3,1), (3,2)
$$
they can either be in $R$ or not be in $R$, leaving us with $6$ yes/no choices. There are $2^6$ ways to make these $6$ choices.