A normal user could set file protection using the Edit File data processing Matrix action (core p. 239):
... You can also use this action to set protection on a file if you’re its owner. To protect a file, make a Simple Computer + Logic [Data Processing] test. The number of hits you get becomes the rating of the protected file. A protected file cannot be read, changed, deleted, or copied until its protection is broken.
This protection could be removed with a Crack File attack Matrix action (core p. 238).
However, normal users cannot use attack Matrix actions so how does a team work with their own protected files?
This will be my first SR5 game so I am fairly new to the system, but from what I have read on Shadowrun forums the Matrix part of the rules has a lot of bugs. It would be nice to get a confirmation from more seasoned players that this is indeed a bug and what would be reasonable solutions within the system.