I finished my first play through a few weeks ago, and during the time I earned quite a few outfits and weapons through the Arcade and Online Weekly Challenges. I started a new play though and noticed that, randomly, two weapons in particular will appear in shops as owned and then disappear from my inventory upon fast travel, and no longer appear in the shop after this. The weapons are the MBP .50 Gold & Steel and the AR-C "Silver & Carbon Fiber". I'm not sure if it affects anything else, but this is kind of annoying and since they were challenge rewards, it's not like I can go back and re-earn them.