I'll try to tell this as well as I can remember. I was doing the first level mining quest where you get 15 dullite, 13 beryl, and 11 sparkly stone. I was using a standard quality axe, the one that costs 500. I started in chad gallows with the dullite, of which I got a total of 17 pieces. Then i went to maharlika heights for the other two types. From the beryl I got a total of 17 as well. Then I continued to mine from the shiny rock. As I got the last few bits I needed, the quest complete screen popped up. As the screen disappeared and the 4 pieces of shiny rock went into my inventory, i saw that all of the rock I had previously had disappeared except for the 4 shiny rock that had just been added.
Also, I saw this once while down a hole, not sure if it happens a lot. When performing action in an underground area, the status bar seems to get hidden by the ceiling part of the dirt foreground if it is close enough to the character.