After revisiting all areas of the game via the bathysphere and making sure that all little sisters have been harvested or saved around Rapture. You have confirmed that all of the sisters have been dealt with yet the trophy/achievement is not unlocking. This may not actually be a glitch. If you have dealt with all of the little sisters but still have not unlocked the trophy/achievement then you need to make sure that you have visited the areas in the game that do not have a bathysphere.
When I played the game I didn’t get the trophy. After revisiting the game I gave up and started a new game I’m on easy to try again. Upon doing this I discovered that there is a little sister in the farmers market that is not listed in the main area where the bathysphere. When you visit the farmers market you will find that the pause menu shows one sister in the area.
There is also the same situation in Olympus heights. A sister is in an area outside of the bathysphere. If you have missed this trophy, go back and check these locations before starting the game again.