This happened to me a day ago while questing.
What I did was, when I collected the first two spots fragments then I abandon the quest.
After retaking and doing it again, I managed to collect the first spot fragment for 4 times. So does the second spot, thus making me skipping the bottom spot (which currently has the bug).
Or try doing it with a friend which has the same quest. Collect the fragment in a spot together until you get enough to skip the last spot.