After you have 9-10 tokens in your inventory the caches stop awarding tokens. That is my experience when clearing lost sectors. Can't get more than 9 tokens in my inventory before it stops (3 per lost sector). If you do another lost sector the cache opens after beating the boss, but no faction tokens are included.
-
you can now only open 2 every 10 minutes to get tokens unfortunately bungie hates fun and removes it when ever its found