use strict;
use warnings;
use Data::Dumper;
my %hash = (
    'Message1' => [ '0X026003', '0X026004' ], 
    'Message2' => [ '0X026007' ], 
    'Message3' => [ '0X026007' ], 
    'Message4' => [ '0X026005', '0X026006' ] 
    );

delete @hash{ grep { @{$hash{$_}} > 1 } keys %hash };
print Dumper \%hash;