I tried to do the same thing on purpose to see if it would happen again. This time I noticed there was 1 on the ground and 1 at the bottom of my inventory wich i could just drag back to hands.
My interpetation of what's happening is that when I logg out and get ut into lotus position(anti-combatlogger) the original rifle gets put on the ground, but a duplicate of it remains to be dragged back to hands.