Welcome SayWhat?!,

Rather than debug your script for you, I hope I can make some suggestions for you to learn to better debug your scripts. Note: these are suggestions and after some years of doing your own debugging your suggestions could be very different than mine.

If your Perl supports it, use the 3 parameter version of open:

  open (my $FALSEF, "<", "FalseFriendsList.txt");
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I like how you name your files, and you can do the same with Perl variables, i.e.

  my %ExistingFalseFriend;    #  or
  my %existing_false_friend;  #  or
  my %Existing_False_Friend;
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This will help your eyes see exactly what you wanted to emphasize when you look at the code sometime in the future. Also, I define a $Debug variable that I set to the level of debugging

  my $Debug = 3;     # 0 - production, 1 - minor debugging, 2 .. 9 for
+ different levels
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This leads to what is needed most in your script -- self-help debugging information. For example why not use a 'foreach' on the hash(or array) to see exactly what you just created.

#while the FF input exists
while (my $line = <FALSEF> )
{
                   # chomp off the new line
    chomp $line;   # chomp could be part of while statement
                   # increment $line
    $falsef{$line}++;
}
  ### Now during debugging print to open log file
  if ( $Debug )        # this could be 'if ( 1==1 )' for testing, your
+ call
  {
        foreach my $key ( sort keys $falsef )
        {     print $LOG "$key\t$falsef{$key}
        }
  }
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Now in your debug log file, you may see that you didn't initialize the hash the way you wanted. Again, my suggestion of 'foreach' could have been replaced by a print statement inside the 'while' loop.

In general, I like your style and I'm sure it will get better and better.

Good Luck...Your on your way!