I'm not sure why you're currently getting error messages, maybe something else is overwriting dbh. But I am concerned about your lack of error checking and your use of prepare (and if this was just a stripped down example, much apologies).

my $dbh = $self->param('dbh') or carp "dbh is not behaving\n";
...
$sth->execute() or carp "problems executing ...\n"
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note bad code showing use of "do" vice prepare deleted - it was just wrong but you probably should try prepare_cached and bind_params.

my $query = "SELECT id FROM table WHERE user = ?";
my $results=$self->query($query, $user )->fetchrow_array;

sub query {
    # Do database query
    my($self, $sql, $val ) = @_;
    
    my $dbh=$self->param('dbh') or die "what's up with dbh?\n";
    my $sth = $dbh->prepare_cached( $sql );
    $sth->execute( $val );
    return $sth;
}
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But maybe I'm all wet and you were just showing a snippet.

-derby Update: nevermind that whole "do" thingy - that only works on non-SELECT sql. drats.