Upon many, many rewatches, I randomly noticed this and my mind is blown! During the fight Ted and Stella have in their room at Shelter Island about how exes shouldn’t be at the wedding, Stella is venting and she says about Tony, “it’s been five years and somehow we still can’t get past it.”
She says WE, not HE. It’s so subtle, but the next scene is when Ted comes back to find Stella gone and a note left for him. Then it cuts to Robin catching Stella and Tony on the ferry together.