I have seen a proof that every relation which is symmetric and transitive is also reflexive.
if $A=\{1,2,3\}$ Then if $R=\{(1,2)(2,1)(1,1)\color{blue}{(2,2)}\}$
here $R$ is symmetric and transitive on $A$ but not reflexive right?
Can anyone clear up this confusion for me?
Every relation that is transitive and symmetric is reflexive on its domain, where the domain $dom(R)$ of a relation $R$ is $$ dom(R) := \{x \mid \exists y\, xRy \} $$ (and where, as usual, $xRy$ means $(x,y) \in R$). This is easy to show: if $x\in dom(R)$, then $xRy$ for some $y$, so $yRx$ by symmetry, and then $xRx$ by transitivity.
The domain of the relation $R$ that you exhibit is just $\{1,2\}$, not all of $A = \{1,2,3\}$.