If you are talking about aspect, then yes: they won't stack but the new aspect will replace the older one! We received a lot of complaints on this so will definitely add a more explicit/noticeable warning on a later update!
Valid suggestion! If a big warning sign is implemented and it still can't sufficiently inform players aspect can't stack, then maybe we should just disable applying duplicated aspect. But doing that will certainly make the game less intuitive and make some effects weird (like archivists, or "the next aspect will have double the effect" -- this one not in the game yet). But hopefully a big warning sign can solve everything!