Well, you didn't actually say _how_ it wasn't working as expected. But I'll take a stab and assume that the last line in file two is being printed to your result set, when you don't want it to be.

But regardless, this code:

#!/usr/bin/perl -l
use strict;
use warnings;

my @fileone = qw/123456 123457 123458/;
my @filetwo = ("123456 foo",
        "123456 bar",
        "123457 foobar",
        "123455 this wouldn't be printed to new file"
        );


foreach my $pattern (@fileone) {
    foreach my $line (@filetwo) {
        if ($line =~ /^$pattern/) {
            print $line;
        }
    }
}
[download]

Gives this result:

123456 foo
123456 bar
123457 foobar
[download]

Which is as expected. You probably need to show us more of your code. I suspect that you're probably missing a chomp somewhere along the line...

Cheers,
Darren :)