What am I doing wrong?

Having written dozens of Perl DBI based scripts/apps/CGI/whatever over the years I'm pretty set in my ways of approaching things like this. So let me show you my method and see if it helps you.

#!/usr/bin/perl -w 
#
# Boiler-plate-ish database pattern
use strict;
use DBI;

my $dbh = DBI->connect("DBI:Pg:dbname=mydatabase",'','')
         or die $DBD::errstr;

my $sth = $dbh->prepare(
qq(
SELECT Count(*) as x from e_annotation_090812.annotation A WHERE A.use
+r IN (SELECT T.Line FROM europhenome_annotation_090812.Temp_table T) 
+AND entity_name LIKE '%' AND evidence_code NOT LIKE ? AND A.centre LI
+KE ?
)               ) or die $dbh->errstr;

# Handwaving $ev_code and $pattern2
$sth->execute ("%" . $ev_code,"%" . $pattern2);

my ($count) = $sth->fetchrow_array();
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Important elements of that code to consider.

1. Use placeholders... you'll be glad you did. DBI takes care of making sure the correct quoting is in place. Prepending or appending the wildcard character works well.
2. The prepare/execute sequence will save you some grief. Especially if you trap errors as I've shown in my example.