(If you don't care for trophies, spare us the lecturing about how pointless they are anyways, thanks.)
I've checked in several boards and apparently, this is an issue a lot of players are having. And don't tell me we didn't find them all, because I played the game three times now, twice with a collectibles guide and I found all 71. The rest is up to 131 together with the shards. In total, it should be 132 if I'm not mistaken. The crystal in question seems to be the one in Chapter 2-2, behind a destructible wooden wall.
If I start the chapter and get to it, the crystal glows blue as if it had not been picked up. But it cannot be picked up. When I reload the checkpoint and go to the crystal again, it's white as if already picked up.
I'd really like to know whether anyone at inXile or Bethesda is aware of this issue, if anyone of them cares and if it will be fixed.