Seen it happen multiple times while leveling various teams, wrote bug reports for them each time. Can't tell you why though. I can tell you that (for me at least), when I do notice there are rewards missing, closing the quest pane and interacting with the NPC a second time will display (and award) the items correctly.

That said, I haven't noticed it recently simply because I've been using the AutoGear addon to auto-select and auto-equip upgrades while leveling to speed things up.