The following code fragment illustrates the problem:

<?php
class Test
{
    public $foo = 'foo';

    public static function getFoo()
    {
        $test = new Test();
        return $test->foo;
    }
}
?>

The first use of $test gets underlined in yellow, and the warning is 'Variable does not seem to be used in its scope'.
Now, I might be wrong, but the line reading 'return $test->foo;' looks like it is using the $test variable, and in the
same scope...

This is the absolute minimum bit of code I can find to demonstrate this bug, but there are plenty of occurrences of the
same spurious warning in my current project.

For example, if I add the following:

<?php
$arr = Array(new Test());
foreach ($arr as $test)
{
    $details = $test;
    echo "<p>{$details->foo}</p>";
}
?>

I get the first instance of $details underlined yellow with the same warning.