I had just built my companion and deployed it for the first time, and I press the “pick up companion button”.
The companion did not return to my inventory (I looked in the “All” section) and returning to the companion station did not return it to my inventory either. I restarted the game and it did not fix the problem.
Using my other character, I can put my companion in the storage box, but I would rather not go through loopholes to use the companion.
I am on Playstation 5. Please let me know if this is a currently known bug and if there are plans to fix it, or if there is something I am missing.
EDIT: I think I may have already found a fix for the issue. If you place your machine companion in the box from one character AND using a second character you pick up the companion using the prompt: it seems to register the companion from the first character as the companion from the second.
Returning the companion from the box to the inventory of the first character and then returning to the companion station with the second character appeared to give the second character the companion back.
My explanation may not be clear, so please ask me questions if you would like.