There's been a couple of times, sometimes it's a mission item for a mission at a different settlement, it doesn't seem to correctly sort that stuff until you land at a settlement where you have an active mission and that's the point where it actually checks to see whether you have mission-critical items and gives you the one specific to this mission.
If you take, say, a sabotage mission, then fly to a different settlement where you don't have a mission, then you'll have the sabotage mission item in your pocket. If you take the sabotage mission and a heist mission, then go to the heist mission location first, you won't have the sabotage mission item in your pocket.
E-breaches are almost always something you have to manually collect, but occasionally, they'll be on you when you disembark whether you asked for them or not.