You applied the patch? You have to return to Resta, open the red chest and use the "Blocked Path Bugfix" item, it will reset the mission.
Viewing post in Mission help section (spoilers)
So, it seems that i had not completed the "unobstruct path" mission, since as soon i accepted it, it was marked as if that was already done and just had to claim the reward. That was the reason of all the paths being blocked.
(i already started another save in which nothing is going wrong before your replied, so i didn't apply the patch, i don't know if that would have helped. Thanks for the help anyways)