It's hard to tell without seeing relevant code, but if the code was short enough likely you would have found the culprit already.

The intervening code might close STDOUT or use select to select a different filehandle:

sub nasty1 {
    close STDOUT;
}

nasty1();
print "everybody keep silent"; # maybe you get a warning that STDOUT w
+as closed
[download]

sub nasty2 {
    open my $fh, '>', 'output.txt' or die $!;
    select $fh; # everybody keep silent
    print "everybody keep silent"; # this shows up in 
}

nasty2();
print "everybody keep silent"; # this shows up in the output file
[download]

Maybe you did not properly create and open your debug filehandle.

Maybe the code that should print stuff never even gets called at all.