Description:
------------
See the code, it explains better than words.
I've explicitly mentioned array_filter(), coz the bug is 100% reproducible with this function, but array_walk/map() works as expected.

Confirmed on 5.6.9-1~dotdeb+7.1 and 5.4.34-1~dotdeb.0
Both are CLI, didn't tested on FPM

Test script:
---------------
$arr=['   ', ' foo   ', '   ', '  bar   ', 'baz   ', '  '];

function something(array $arg)
   {
      array_filter($arg, function(&$el){return strlen($el=trim($el));});
   }

var_dump($arr);
something($arr);
var_dump($arr);

Expected result:
----------------
Both var_dumps should print the original array

array(6) {
  [0]=>
  string(3) "   "
  [1]=>
  string(7) " foo   "
  [2]=>
  string(3) "   "
  [3]=>
  string(8) "  bar   "
  [4]=>
  string(6) "baz   "
  [5]=>
  string(2) "  "
}

Actual result:
--------------
However the second var_dump actually prints the modified one

array(6) {
  [0]=>
  string(0) ""
  [1]=>
  string(3) "foo"
  [2]=>
  string(0) ""
  [3]=>
  string(3) "bar"
  [4]=>
  string(3) "baz"
  [5]=>
  string(0) ""
}

despite $arr was passed to something() by value, not reference.