The one thing that drives me mad with Fallout games is that you basically have to play them by spoilers unless you want to miss out on a whole lot of rewards due to quests not having a proper flowchart.
For example, take the FO NV quest There Stands the Grass in Vault 22.
If you explore Vault 22 before finding the mission (which is very likely, as Vault 22 is actually between Goodsprings and the base), you keep finding Keely's notes but Keely isn't in the cave. You can however download the research data anyways. If you then find the quest, you have the option of turning in the data immediately, thus instantly ending the quest poorly, or you can return to Vault 22, help Keely destroy everything and finish the quest with another poor reward, because for some reason the data you downloaded earlier disappears from your pipboy.
Here's how the quest goes down if you accept it first, then raid Vault 22
1. Accept mission for data
2. Accept side mission to find Keely
3. Get the data
4. Find keely, agree to destroy everything
5. burn the spores
6. return to keely, convince her to not have you erase the data with a 70 science check
7. return to camp, get rewards for both.
6 did not appear for me. Because the data suddenly stopped existing. I also could not download it again from the terminal.
It makes no sense that you can get the data, but Keely isn't in the cave (yet her notes are all over the place). And FO3 and NV have quite a few missions that simply won't work out if you just stumble across them and do them in reverse.