When you copy a hashref into another scalar, you are copying a reference to the same hash. This is similar to copying one pointer into another, but not changing any of the pointed-to memory.
You can create a shallow copy of a hash easily:
my $copy = { %$source };
The %$source bit in list context will expand to the list of key value pairs. The curly braces (the anonymous hash constructor) then takes that list an creates a new hashref out of it. A shallow copy is fine if your structure is 1-dimensional, or if you do not need to clone any of the contained data structures.
To do a full deep copy, you can use the core module Storable.
use Storable 'dclone';
my $deep_copy = dclone $source;