If you're talking about arrays as hash values, just use push.

push @{ $Hash_filematches{ $filename } }, grep( /\/\Q$file_name\E#/i, 
+@{
+ $Hash_filenames{ $filename } });
[download]

That'll even work if $Hash_filematches{ $filename } doesn't exist yet, when this line is run, thanks to autovivification.