The remaining issue will be that 1.10.l0 also matches lines that match 1.10.1040 To resolve this try something like the following

use strict;
use warnings;
open(my $data_1 ,"<", "data1.dat");
my %stubs;
while (<$data_1>){
   chomp;
   $stubs{$_}=0;
}
close $data_1;
open(my $data_2 ,"<", "data2.dat");
while (<$data_2>){
   chomp;
   for my $stub (reverse sort keys %stubs){
      if ($_=~ /\Q$stub\E/){
         $stubs{$stub}++;
         last
      }
   }
}
for my $stub (sort  {$stubs{$a} <=> $stubs{$b}} (keys %stubs)){
   printf "%-10s: %d\n",$stub, $stubs{$stub};
}

__OUTPUT__
1.10.220  : 1
1.10.1040 : 1
1.10.10   : 3
1.10.150  : 3
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By using the reverse sort on the keys of %stubs you can guarantee a "longest match only"