my $file_count = @ARGV;
foreach my $key1 ( keys %seen ) {
    if ( @{ $seen{$key1} } >= $file_count) {
        print join( "\t", @{$seen{$key1}});
        print "\n\n";
    }
}
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This still doesn't make sense. If you add print "File count is: $file_count \n"; You'll find that $file_count is always 0, because after reading the files with while (<>), @ARGV is always empty. And you check the size of the array in $seen{$key1}, but it always is 2 (there are two elements, Key, and Sum).

When you use while (<>) to read from a list of files, the current file is $ARGV.

# At the top of the file
use constant { 
    Key => 0,
    Sum => 1,
    Count => 2, # Remove this if you don't use the total count
    Files => 3  # Should be 2 if Count is not used.
};
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# In the read loop
$seen{$key1}[Key] //= $key;
$seen{$key1}[Sum] += $value;
$seen{$key1}[Count]++;         # Total count for the number of times t
+his value exists
$seen{$key1}[Files]{$ARGV}++;  # Count in this file
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You don't seem to want a particular format for your output (because you changed it when adapting my proposition), so you could try just dumping the whole structure using either Data::Dumper (nothing to install) or YAML (needs to be installed, but can be nicer to read).

use Data::Dumper;
while (<>)
{
  # Your code here
}
print Dumper(\%seen);
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Or

use YAML;
while (<>)
{
  # Your code here
}
print YAML::Dump(\%seen);
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