In my experience, you miss events when you trigger a particular development – at Waukeen's Rest, when one of your party says "Something's burning" – and then change zones before proceeding. I had a similar experience when I skipped the early Mind Flayer/fishers interaction and tried to go back later, and when I went too far towards the Goblin Camp before talking to Volo in the Druid Grove – it was nothing to do with resting, just a timer or trigger that fires when you reach a certain point.