Amethyst Nexifera Tags Impossible to Collect, Making New Mods Also Impossible to Collect

Please confirm that you are leaving the Deimos landscape using the door back to the Necralisk?  You're not using Abort? Inventory progress is saved automatically on the landscape but it is not instant, so if you're using Abort immediately after collecting the Amethyst Nexifera then it will not save properly.

Also, how are you collecting the Nexifera, using the Tranq Rifle or a sleep power? (Which one?)

As a trouble shooting step, I bet if you spend at least 1 minute fishing/mining after you catch your Amethyst Nexifera, that it will save properly.