I can not reproduce your results, in part because your results are strange.

It would help if you posted a complete example that demonstrates your problem, and enclose that in <code> tags. Here's what I used to test:

use 5.010;
use strict;
use warnings;
use Carp;

my $var = 'QeTEv2804';
printf "%s.\n", $var;

open my $debug, '>>', 'debug.txt' or confess "Couldn't open file: $!";
printf $debug "%s.\n", $var;
close $debug;
[download]

debug.txt:

$> hexdump -C debug.txt
00000000  51 65 54 45 76 32 38 30  34 2e 0a                 |QeTEv2804
+..|
0000000b
[download]

In your output, those control characters are NULs, not line endings, and they somehow come before the `.' in your output, suggesting they are part of $var itself. If I append NULs: $var = "QeTEv2804\0\0\0"; and re-run the above script, the output still looks like this, because those \0s are unprintable:

Are you sure this is your actual code? Something seems fishy.

Edit: Took out irrelevant info from above paragraph and added example that reproduces the OP's result.

Another thing I'd suggest is to always use the 3-argument open with lexical file handle, as I did in my example. It won't affect your results in this case, but it's a best practice.