It's ok not to read the thread, it's not ok to induce misinformation and/or create confusion
The issue is related to Crystaline Shards, an issue that started to manifest after April Patch, that was corrected in the September Patch and that apparently appear again in September Patch Update 2
The issue is about a healthy percentage of Shards disappearing (vanishing) after being shot from the spikes
Edit: the above issue was happening on PC.
On XBox, the issue was quite different: a certain shape of Shards (colloquially known as shuriken shards) were falling through the ground.
It was fixed in September Patch - no idea if it came back with Update 2
No shurikens falling through the ground after patch #2, no shurikens stuck at the top of the trees. Actually there are no shurikens at all after patch #2, only sea urchins, plus a certain fraction of crystal shards annihilating if you are shooting at them (maybe these would be the shuriken types, if they ever managed to appear after having been shot at, which they don't).
The issue is clearly visible in the video I've already posted before:
The video was recorded after patch #2. I visited the bio sites a few days before patch #2 as well (but after the Sept update) and the crystal shards used to work just fine that time (none of them were annihilating), but sadly I don't have a recording of that.
The issue cannot possibly have anything to do with the respawning of the shards for the following reasons:
1. When I visited the sites the first time (before patch #2), I only visited a grand total of 2 sites on 2 planets (ones giving Tellurium and Ruthenium), and when I went there the second time (after patch #2), I visited multiple sites on all relevant planets, and the bug was present everywhere.
2. A completely exhausted site (where the materials had insufficient time to respawn) would behave very differently: the shards wouldn't be annihilating for the simple reason that there wouldn't be anything to shoot at there in the first place.