What I did:
Had two projects selected in the project sidebar, so that I could see the notes in both in the central column.
Selected an event in the calendar, created a new note
A dialog asked which project the note should be added to. I selected one of the projects.
What happened:
Two notes associated with the event were created in the selected project
What I expected:
One note
Things that might be helpful to know (Agenda version, OS and model, etc):
Version 18.3.2 (295) - Mac App Store
Edit: I’ve since deleted the Notes created, removed the Agenda links from the event in Fantastical, opened Mac Calendar App to force refresh (hopefully), restarted Agenda. And then tried to create a note associated with the event again. Two notes created again - even though I hadn’t selected any project in the sidebar.