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You have to scan those with a Scanner, which you have to make using the fabricator.
If you mean things like res- Quarts, metal scrap, acid mushrooms and the like... if you can't left click to grab those when your PDA shows inventory slots open... you have a bug. Try saving and restarting. Verify files through Steam file verification. Start a new game and see if the bug persists. All things to try.
And are you playing in Experimental or Stable build? Were you able to pick upitems before or scan fragments before? And does your system exceed the minimum specs by a decent amount? Or even meet them at all?
Because the game is still in development and some parts, like the Scanner room, are not implemented into the game yet. It's Early Access. They have parts in that will be made functional as the game development prgresses to completed stages. They said they are shooting for August, but can't be sure they can complete the full game the way they want it in that short amount of time.
Patience. Those frags will either be implmented by full release version. Just gotta be patient.