For some reason, the game keeps forgetting the stuff I did already (ex. being asked to build a trade route when I did it already)
Yeah, others have noticed the Trade Route reappearing, that one is most likely not setup correctly.
You can let me know if you have other examples for this happening as well.
For other situations it's less obvious if the events should happen once or not, but I think that the tree telling your mom about what you did is something that should happen once
That one is intentional, but maybe I'll change it