A pretty common logic error is forgetting to explicitly check all expected values against the variable:

use strict;
use warnings;

my $foo = 'boo';
if ($foo eq 'goo' || 'moo') {
    print "$foo\n";
}
[download]

when this is really desired:

if ($foo eq 'goo' || $foo eq 'moo') {
[download]

Obviously, this is not unique to Perl, but I do see it quite often.