This is easily done:

#! perl
use strict;
use warnings;

my $file1 = 'file1.txt';
my $file2 = 'file2.txt';
my $error = 'error.txt';

open(my $in1, '<', $file1) or die "Cannot open file '$file1' for readi
+ng: $!";
open(my $in2, '<', $file2) or die "Cannot open file '$file2' for readi
+ng: $!";
open(my $out, '>', $error) or die "Cannot open file '$error' for writi
+ng: $!";

my $lineno = 1;

while (my $line1 = <$in1>)
{
    my $line2 = <$in2>;

    printf $out "Error:lineno:%d please check mismatch\n", $lineno
        unless $line1 eq $line2;

    ++$lineno;
}

close $out or die "Cannot close file '$error': $!";
close $in2 or die "Cannot close file '$file2': $!";
close $in1 or die "Cannot close file '$file1': $!";
[download]

However, why reinvent the wheel? If the format of the output is acceptable to you, prefer a module such as Text::Diff:

use strict;
use warnings;
use Text::Diff;

my $error = 'error.txt';
my $diff  = diff "file1.txt", "file2.txt";

open(my $out, '>', $error) or die "Cannot open file '$error' for writi
+ng: $!";
print $out $diff;
close $out or die "Cannot close file '$error': $!";
[download]

Output:

--- file1.txt    Tue Aug 26 17:12:02 2014
+++ file2.txt    Tue Aug 26 17:12:22 2014
@@ -1,6 +1,6 @@
 Figure 1.
-Somatotropes are organized into.
+children with acquired organized into.
 Figure 2.
-Comparing two xml files organized into.
+Severe anterior hypoplasia,
 Figure 3.
 Somatotropes presentation of GH1,
[download]

Hope that helps,