To reproduce:
Create New Project - PHP 5.4.
Replace index.php with following:
<?php
class A
{
public function get() {}
}
class B
{
public function get() {}
}
$a = new A();
$b = new B();
$a->get();
$b->get();
?>

Right-click get() in class A and choose Find Usages. (Find Usages checkbox checked, Find Overring Methods unchecked), click Find.

Result:
Usages of get [4 occurrences]
PhpProject1
index.php
      4:  public function get() {}
      8:  public function get() {}
    13:  $a->get();
    14:  $b->get();

Expected result - 2 occurrences - definition in class A and one usage: $a->get();


Product Version = NetBeans IDE 7.2.1 (Build 201210100934)
Operating System = Windows XP version 5.1 running on x86
Java; VM; Vendor = 1.6.0_23
Runtime = Java HotSpot(TM) Client VM 19.0-b09