Should I discourage using messaging apps for research group communication? I've seen a growing trend in later years: graduate students discussing research questions through Facebook or Whatsapp like it was the standard channel to solve all kind of issues (Could you send me script x? Where are the data y? How did you perform analysis z?) 

These questions are at center of research reproducibility and I'm worried  using tools as ephemeral as Facebook messenger may cause me headaches in the future. What if the conversations are deleted and later I can't track a important exchange? (or worst case scenario, dig a case of scientific misconduct, like purposefully obscuring the origin of data?). Emails and other utilities like Google forums provide, in my opinion, a better platform to report issues, get them rolling until they are solved, and finally keep a record of the exchange. On the other hand, Facebook Messenger seems linear and messy, unsuited for this kind of purpose.

Maybe I'm getting old too quick, but should I discourage this practice? For instance, by promoting other tools like Google forums. Has anyone had a bad research experience because someone used Facebook or WhatsApp for scientific communication? How did you address the issue?
No. If you are worried about your colleagues being able to delete the messages from Facebook / Whatsapp, how do you cope with them calling each other? Or worse: actually talking, walking to their office and just copying files? 

I'm all in favor of making communication easier, as insufficient communication between researchers is wasting millions of hours every year. But it should be with the goal of facilitating communication, you'll never get an environment that's completely traceable. That a wiki will have some kind of versioning or history will be an additional benefit, not a reason to use a wiki. 

And besides, who's going to check all that communication? Scientific literature is full of fraud and misconduct that's in plain sight and not corrected. Errors in literature are there because people do not care and have no time, not because they lack the forensic tools.