From the weekly update

I thought that this was fairly notable. Be careful when using the app to put things in the vault. "Last week, we announced an update to the Destiny Companion that enabled you to equip or vault your items on Bungie.net... ...we have heard reports that players are losing items when transferring items using the Companion app. While we investigate this issue, please be sure to check all Inventories amongst your characters, and to use caution when transferring items during mission countdown timers and load-ins for maps."