You are absolutely correct that you can very easily create “a whole bunch of separate references to the same thing,” instead of references to different things.

“Holy EQUIVALENCE, Captain Fortran!”

I confess that I sometimes use the Storable module (or nowadays, Clone to explicitly create a “carbon copy” of whatever I need to be damm sure is a unique copy of a thing.   So, I might say... push @myarray, dclone($foobar).  It might not be “efficient,” but generally that is not so important to me as “obvious reliability.”

P.S.:   As you play “data-structure games,” be mindful of the weaken subroutine in Scalar::Util.   If you might be constructing circular-references between data structures, be certain that one or more of the references are “weakened” so that all of the self-referential data structures eventually will be garbage-collected.