I've noticed this feature: if you have accidentally found some item before it appeared in your quests and you are able to combine a collection with this item already - do it! It will sort of "verify" that you had this item and the quest will be completed. And don't worry about the 6th step of each quest-group, which is "combining a collection" - this one somehow solves itself right when it appears, if you have at any point combined this collection.

Note: Use this tip with caution if you do not have extras of the remaining items as you may struggle to obtain those! This tip is best used when it is the last item in a collection.