The problem is that you are applying ceil to the outer expression. Try to rewrite it as:

$charges = 9;
$cost = 100;

echo ($cost + ceil($cost * $charges / 100)) * 100;

This outputs 10900 as expected.

UPDATE

As @cars10m suggested, simplifying the expression does help:

echo ceil($cost * 100  + $cost * $charges);

UPDATE 2

You can also use BCMath library to do precise math:

bcscale(6);
echo ceil(bcadd(bcmul($cost, 100), bcmul($cost, $charges)));