Welcome to the forums, edmund36.
Yes, you've missed out on a lot - there are challenges to complete, GPS caches to collect, relics to find and tombs to raid. You must have missed some to complete the game at 69%.
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If you've missed out on collecting GPS caches and completing the challenges, it should be possible to load your last save point and pick up anything missed between the camp sites. Unfortunately, some time-sensitive items in the story are missable such as getting the Chatterbox trophy. If you avoid talking to all crew members whenever the opportunity presents itself then you'll have to completely replay the game to unlock the trophy, assuming you're playing the game for its trophies.
If you're in need of a Tomb Raider trophy guide, here's one that should be helpful. Unfortunately, the other percentage of the game consists of multiplayer matchmaking.
Because I missed chatterbox on my first playthrough I have one more playthrough left before I hit MP. Is it really that bad?