Why are 31.8% of retracted papers not noted as retracted?
The only reasonable answer I can think of is "laziness".

In particular, when journals existed only in print, the only thing a journal could do when it retracted an article was to print a notice in a new issue.  There was no way to modify or recall issues that had already been sent to subscribers.  Some journals may still have retraction policies from that era, which don't contemplate trying to actually do anything to the original article.

Note that the article you quote is almost four years old, so matters may have improved in the meantime.