About leader challenge:
https://forums.cdprojektred.com/index.php?threads/quest-contract-during-the-faction-challenge-doesnt-count-for-the-achievement.11005756/
I got an answer for my ticket:
The issue with challenge-related contracts not progressing when completing quests in the current challenge was fixed. We are currently working on retroactively updating the progress made before the fix went into effect for the affected players.