If I understand your goal and data, here's a method that uses two hashes -- one to keep track of how many different "Obj1" things there are, and the other to keep track of the distribution of "Obj2" things. It handles all three categories of "Obj2" things (common to both Obj1 things, unique to each), but it requires that the input be pre-sorted: 
use strict;

my %obj1found;
my %obj2found;
while (<DATA>) {
    if ( / HIT \s+ 
          (\S+ \s+ [\d.]+) \s+ 
          (\S+ \s+ [\d.]+) /x )
    {
        my ( $obj1, $obj2 ) = ( $1, $2 );
        $obj1found{ $obj1 }++;
        $obj2found{ $obj2 } .= " $obj1 "
            unless ( $obj2found{ $obj2 } =~ / \Q$obj1\E / );
    }
}

my $match_all = join( '  ', sort keys %obj1found );
   # note: two spaces between elements

print join( "\t\n", "\nList of Obj2 things found in all Obj1's:",
            grep { $obj2found{$_} =~ /\Q$match_all\E/ }
            sort keys %obj2found ), "\n";

for my $obj1 ( sort keys %obj1found ) {
    print join( "\t\n", "\nList of Obj2 things found only in $obj1:",
            grep { $obj2found{$_} =~ /^ \Q$obj1\E $/ }
            sort keys %obj2found ), "\n";
}

__DATA__
HIT object1 563.43.78 object3 123.89.7777 
HIT object1 563.43.78 object10 123.89.7777 
HIT object1 563.43.78 object2 453.78.122 
HIT object1 563.43.78 object5 457.8888.1 
HIT object1 563.43.78 object4 123.89.7777 
HIT object1 563.43.78 object6 566.2222.11 
HIT object2 563.43.78 object3 123.89.7777 
HIT object2 563.43.78 object7 456.222.1111 
HIT object2 563.43.78 object8 990.7777.66 
HIT object2 563.43.78 object5 457.8888.1 
HIT object2 563.43.78 object13 123.89.7777 
HIT object2 563.43.78 object9 1223.333.111

[download]

This approach would generalize to any number of distinct "Obj1" things. If you have more than two, you might want to look at groupings other than "found in all Obj1 things" and "found only in a single Obj1 thing" -- that's "left as an exercise..."

In reply to Re: How to check for duplicate entries by graff
in thread How to check for duplicate entries by Angharad

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