For example PHP's PDO library makes it less convenient to supply parameters to a query the safe way than it is to do it the unsafe way. This is not necessary as can be seen from the excellent Ruby library called Sequel where it is just as easy to do things the safe way.
Another example is PHP itself being a template language, but which lack of automatic escaping makes it very dangerous to use. Since just one missing escape call in the wrong place can fuck up your day. To be fair PHP is not the only one who has fucked up here. This is also an issue with Ruby's ERB templates in the standard library, but fortunately Rails has added automatic escaping to its ERB templates.
One important thing about designing safe software is to make it easy for the end users to do things the right way, and here I think PHP has done a pretty poor job.