PHP filter is a great filter. It gives you a lot of flexibility. But it has a lot of disadvantages too. One of them is that it makes your code harder to debug.
One of those hard debug sessions occurred lately when the following happened. Cron always stopped running when it was going to index this one node. It also redirected to some page. Weird.
What was happening? The node was a page. The body was having the PHP filter on and the following code was in that body:
<?php drupal_goto("node/add/story"); ?>
What does this have to do with search indexing you ask? Well, when the search indexer is going to index a node, it first runs all filters on your body, and it's the result of that that is getting indexed. So if you're writing PHP code, that code is run when the indexer comes along. Even "non-text generating" code, like the redirect in this case.