In typical algebra textbooks, the elements of the structures presented are explicitly defined: for example, the n-th Symmetric Group, $S_n$ may be defined as containing precisely the permutations on the set $\{1, \ldots, n\}$, with function composition as its binary operation.
However, this is not a given, and another author may choose to define $S_n$ as containing permutation matrices, or using $n$-tuples, or whatever.
Thus, there appear to be all these $S_n$'s floating around, which is contrary to ordinary phraseology (i.e "Let $S_n$ denote the n-th symmetric group"). What is meant by such a phrase is something along the lines of: "let $S_n$ denote a group isomorphic to anything else one might imaginably call $S_n$, where in the context of where it will be used, the precise elements of the group do not matter."
But, I would say that this is an incorrect use of the word "the", and a more appropriate word would be "a". However, this all rests on what you believe: whether $S_n$ refers to a class of isomorphic groups, or whether it picks out a very specific "canonical" representation of it. So: which of the two is it?
You are absolutely right ,it is a misuse of the word "the"in the sense of the object satisfying some displayed property . You could say for a set A , any set of n objects, that S(A) (or $S_n(A)$ ) is THE set of all bijections of A . That would satisfy me .