Losing official documents is a very serious business. If IRCC admitted so candidly that they routinely lose application documents, then would be an investigation, MPs would look into this. Sending another application is not a simple matter if a police certificate is required: IRCC requires only original police certificates, and it could take weeks if not months to obtain those certificates. Without mentioning the fact that, as mentioned by other users in this forum, immigration applications contain more than enough information to steal someone's identity (name, address history, employment history, passport, several IDs, SIN) and losing them lightly is reckless at best.
The approach "if we lose your application just send another one" would simply be unacceptable, IRCC officers would get into a lot of trouble if this were true. I don't buy this explanation.