You did not specify what to do if the file is missing in one of the hashes. The following code informs you about all the possible situations:

#!/usr/bin/perl
use warnings;
use strict;
use feature qw(say);

my %size1 = ( 'autorun.inf'  =>  42,
              'autoexec.bat' => 118,
              'eicar.zip'    => 186,
            );

my %size2 = ( 'autorun.inf'  =>     42,
              'autoexec.bat' =>    119,
              'ibmbio.com'   => 234186,
            );

my %files;
undef @files{keys %size1, keys %size2};

for my $file (keys %files) {
    delete $files{$file}, next if exists $size1{$file}
                              and exists $size2{$file}
                              and $size1{$file} == $size2{$file};
    $files{$file} = 'Missing in 1', next unless exists $size1{$file};
    $files{$file} = 'Missing in 2', next unless exists $size2{$file};
    $files{$file} = 'Size changed';
}

for my $file (keys %files) {
    say "$file\t$files{$file}";
}
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