However, my question is actually how can ARENA COUNTS show 69084 REF-Tie::RefHash::Weak when all the adding all the scalar(keys %HASHS) of all the hashes using Tie::RefHash::Weak, scalar(keys %EACHHASH) added together is much much less than 69084.

That is why they call it "memory leak" :) The "arena" goes through internal perl structures to see which structures are allocated. As long as variable is accessible from the user code, it is "good" structure. The problem comes, when the structure is not accessible from user code. This structure is then "leaked". So, if you have a leak, then you won't be able to see leaked structures from your perl code. Of course in this case your count won't match the count of "arena".