Well, your SMS'es and contacts (and pretty much everything else too, including email addresses, calendar events, geolocating POI, music metadata, picture metadata, whatever!) are stored in a central database called "tracker database"

Now if you have bad-behaving software, like some buggy messaging applications (facebook/twitter/whatsapp/whatever) it well might happen that your database gets twisted, some ID's not pointing to where they are supposed to....

It will create a lot of problems that can manifest in very off behaviour, like loss of messages and contacts, or duplication of those.

Well known problem with N9, however as it is not updated any longer there really is no hope getting fixes for the problems.

How to avoid; Take frequent backups, and when something goes crazy, restore previous backup.