I have witnessed this now with multiple areas. Crucible and two different factions. I have ranked up more than once before picking up the packages and end up only getting one package. Not everything in one, but the effects of one package. I did this today with Crucible and got a gun a ship and motes of light/whatever other material it was. I did a mote of light dead orbit rank up and not thinking about it, did two ranks before opening a package. Same issue. While life does move on, it is a little frustrating when you are trying to get some better gear and you end up wasting the rank up.