Fellow forum readers, I submitted this question to Ubisoft support. I decided to include it here in case a resolution is found.
Dear Ubisoft Support and Ubisoft Montreal,
During a game of AC: Black Flag on the PS4 I noticed that during my final play through, 3 of the last trophies related to the main storyline failed to unlock. I went online and searched the forums and noticed that other players were experiencing the same problem. I also noticed that during my final play through of Sequence 12 and 13, my system briefly lost its internet connection and the additional online content, such as shared events, were not available. Seeing as how every other trophy unlocked correctly, these two events happening together might not be coincidence. I'm not sure a resolution to this issue exists, but hopefully this helps you investigate the issue and assist other players with similar problems.
I realize that other players were asked to replay the game using a new save game. Given that I have invested several hours into the first play through I find this resolution unlikely. I have also retried re-installing the game files, replaying the chapters through the progress menu with no success.
I am a fan of the series and this was a sour end to an otherwise memorable game and excellent ending!
I hope you find a solution, if not for us, but for future players of the game.
All the best,
In addition, I forgot to mention that while the final gold trophy for completing sequence 13 did not pop, the UPlay achievement for completing sequence 13 did. Strange.