its not just BO's, its also some item rewards not ending up in inventory. Also the missing BO's are not in the assignments tab. Items and BO's are just not being delievered at all. Has nothing to do with being in space, on SB, planet side, hailing vs actually turning in mission to in person/character.
Just report it every time it happens. Its no a huge issue, but it still needs to be delt with soon.