If you're referring to the messages that keep popping up telling you the faction allegiance nodes have proc'ed when they already have then it has something to do with the Ishtar Collective App - every time I have the app open on my iPad I get the messages pop up, if I close the app then they stop.
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Nope....I have nothing connected to destiny other than this app and I get the faction completion and multiples records notifications about every 10 minutes or when I land on a destination
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I have the same problem just using the official app.
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I tried it with the official app (it was recently updated) and wasn't able to reproduce the effect, but every time I loaded the Ishtar app up popped the notifications in the game. I hope that an update for Ishtar (or a fix in the game) can be released as I really like using the Ishtar app - it's infinitely better than the official one.