Plot hole: When Henry and Ellie are cornered in the launch tower during the 'Toppat Recruits' and 'Pardoned Pals' routes, the former goes back in time so that the soldiers that apprehended them were never recruited and therefore the main characters are no longer cornered in the present. However, this should simply cause different people to try to stop them, not an entire removal of the threat.
Plot hole: When Henry and Ellie are cornered in the launch tower during the 'Toppat Recruits' and 'Pardoned Pals' routes, the former goes back in time so that the soldiers that apprehended them were never recruited and therefore the main characters are no longer cornered in the present. However, this should simply cause different people to try to stop them, not an entire removal of the threat.