Control Points that have been claimed by the host or FNIX are only appearing as Neutral for players that have joined the session afterward. Resistance bases appearing as neutral cannot be fast traveled to. Furthermore, if a FNIX base appearing on the map as neutral is destroyed, the structures persist and the base destruction does not count. This means no rewards for anyone that has joined after the FNIX base was created.
As far as I’m aware, that is the full extend of the issue, which is myself and some friends have experienced on PC, and it’s been happening since the companion update.