I just finished The Witcher 3 and I have a problem because at the very end after talking to Emhyr it takes me to the white orchard, it pops up that the mission from the well has not been completed all the time until talking to the villagers, an unfinished quest pops up, although before the end of the fight with all commanders it is completed. this annoys me because I try to have everything in completed missions, and unfortunately it's not possible. Loading a previous save does nothing, because when I complete this task, the task becomes incomplete, as if it jumps out of completed.
This is an old issue. Unfortunately, this is not a game like so many others (Assassin's Creed, FarCry, etc.) Many quests in TW3 are exclusive. Meaning: it branches. At certain points, if you choose to do A, you cannot do B. There will be whole quests, dialogues, etc. that simply will not occur because other, opposite things occur instead. In order to see the other possibilities, you would need to start a new game and make different choices.
So, there's no way to 100% the game in a single playthrough.
The other thing is that the journal system does seem to "fail" already "completed" quests at weird times. My best guess is that this is a sort of failsafe in the engine that prevents it from creating infinite loops or quest bugs later in the game. Irksome, perhaps, but probably better than not being able to complete a playthrough or begin an NG+.