$Hash_filenames{$plf}=@file_lines;

An array evaluated in scalar context returns the number of elements it contains.

A hash element is a scalar. It cannot contain an array. It can contain a reference to an array.

Fix:

my @file_lines = <$match>; 
$Hash_filenames{$plf} = \@file_lines;
[download]

or

$Hash_filenames{$plf} = [ <$match> ];
[download]

$Hash_filematches{$filename}= grep( /\/\Q$file_name\E#/i, $Hash_filenames{$plf} );

• $Hash_filenames{$plf} is a scalar, so your grep is going to return at most one item.
• You call grep in scalar context, so it returns the number of matching items rather than the items themselves.
• You never assigned a value to $plf.

Fix for the first two:

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

Sorry, I don't have time to understand what you are trying to do in order to propose a solution for the third item. But maybe knowing what the problem is will help you.