That's the way it's designed - Haven's weapons requisition is a unique introductory quest, which is why it appears in your journal as completed. After that, the requisition quests you receive from the officer are randomly chosen (from a selection of 5-6 per area, I think), don't appear in your journal once finished, and can repeat. If you don't like the requisition quest you receive, you can save/load before talking to the officer and you'll likely get a different one.
They are also endless (the officer will never stop giving you quests), so it's not recommended that you keep taking them on. Also, if you complete an area many of them are unable to be finished and will stay in your journal forever, because they depend on enemy spawns in the areas, and many enemies stop appearing after you finish the main quest in an area.
My advice - at most, take on and finish maybe 3-4 of them per area for the inquisition points, then stop accepting them. Or just don't take on any of them at all.