I started to come up with a solution much like BrowserUK's, though not quite as elegant, and I decided to move on since his works well enough.

In order to see what was going on, I wanted to run your code. In doing so I fixed all the scoping errors (the 'strict' pragma should have been made the default behavior in like 1996), corrected the whitespace issues, removed unnecessary comments, and closed your filehandles after they were done being used. In case anyone else wants to copy/paste a working version of the original code (which uses Inline::Files), here it is:

use warnings;
use strict;
use Inline::Files;

#open(AB, "try_fimo.txt")  || die("cannot open");
#my @data = <AB>;
#close(AB);
#chomp(@data);
#
#open(BC, "try_fimo2.txt") || die("cannot open");
#my @data2 = <BC>;
#close(BC);
#chomp(@data2);

my @data = <AB>;
my @data2 = <BC>;

my ($t1, $t2, $t3);
my (@tf1, @seq1, @dis1);
my (@tf2, @seq2, @dis2);
my (@tf3, @seq3, @dis3);

foreach my $line (@data) {
  foreach my $line2 (@data2) {
    if ($line2 =~ /(.*?)\s+(.*?)\s+(.*)/) {
      $t1 = $1; # eg. in first row from file2 i.e. ABC, it will first 
+take A followed by B & C 
      $t2 = $2;
      $t3 = $3;
    }

    if ($line =~ /(.*?)\s+(.*?)\s+(.*)/) {
      if ($1 eq $t1) {
        push(@tf1,  $1);
        push(@seq1, $2);
        push(@dis1, $3);
        # print $1,"\t",$2,"\t",$3,"\t";
      } elsif ($1 eq $t2) {
        push(@tf2,  $1);
        push(@seq2, $2);
        push(@dis2, $3);
      } elsif ($1 eq $t3) {
        push(@tf3,  $1);
        push(@seq3, $2);
        push(@dis3, $3);       
            }
    }      
  }
}

for (my $i = 0; $i < @tf1; $i++) {
  for (my $j = 0; $j < @tf2; $j++) {
    for (my $k = 0; $k < @tf3; $k++) {
      if (($seq1[$i] eq $seq2[$j]) && ($seq1[$i] eq $seq3[$k])) {
        if (($tf1[$i] ne $tf2[$j]) && ($tf1[$i] ne $tf3[$k])) {
          print $tf1[$i],  "\t",
                $seq1[$i], "\t",
                $dis1[$i], "\t",
                $tf2[$j],  "\t",
                $seq2[$j], "\t",
                $dis2[$j], "\t",
                $tf3[$k],  "\t",
                $seq3[$k], "\t",
                $dis3[$k], "\n";
        }
      }
    }
  }
}

__AB__
A seq1 20
B seq2 25
B seq2 80
B seq1 40
C seq1 25
D seq2 30
E seq2 45

__BC__
A B C
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