I cannot not recover your issue. If I run the code provided (after adding use Carp 'cluck';, my $job_type = 65;, and a closing quote on your line 4, I get the output on STDERR:

business_unit:  at fluff.pl line 7
business_unit: D at fluff.pl line 7
business_unit: D at fluff.pl line 7
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I suspect your issue is that what you actually mean to have is something like

use strict;
use Carp 'cluck';

my $job_type = 65;
my %bj = (64,'D', 128,'A', 256,'H');
foreach my $flag (keys %bj) {
    if ($flag & $job_type) {
        my $bu = $bj{$flag};
        cluck("business_unit: $bu");
    }
}
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The difference here is that I am now only outputting when the if condition is true; your if applied only to the assignment, not the cluck.

Update: Jenda also has a plausible explanation, if Re: Bitwise & not working correctly in CGI script is correct. This makes sense if you are pulling the string out of $cgi->param, which contains only strings. You can numify the result using my $job_type = 0+ $cgi->param('job');, for whatever those variables are called locally.