You can find a list of all the permit-locked regions in the
permits list thread in the main forum.
None of the reasons for the regional permit-locks have been made known. None of the permits can currently be obtained by any known means.
FD have officially said in the past that "all the permits in the game, are in the game for a reason". It is generally assumed that these locked regions, some of which are much larger than the Bubble of human-occupied space, are the homeworlds of the Thargoids, the Guardians, other Aliens (friendly or hostile), the remnants of the rogue sentient AI, or "lost colonies". They are therefore locked until FD are ready to unveil them, because the content intended for those sites is not yet written into the game (in other words, if you went there now, their planets would be empty).
Keep an eye out for any changes to permit-locked sectors i.e. new sectors suddenly getting locked, or old sector-locks suddenly disappearing. That may be our first and only warning if FD decide to secretly reveal "mysterious things".