Cavendish does hesitate for a moment with around 50M to go. I noticed this too. It's because he had nowhere to go.
Cavendish is on Van Aert's wheel with Philipsen on the right, and the barriers on the left. Tunnesien is doing the lead out for WvA. When Tunnesien pulls off with 200 to go, Philipsen has to go right of him. Cavendish sees/senses that and tries to go around WvA at the same time, but there's no room on the left and Philipsen got around Tunnesien and re-established himself on the right side of Van Aert before Cavendish could make that move. It was at that point that Cavendish hesitated for just a moment and then decides he can only go on the left, but by then it was too late... WvA and Philipsen were already pulling away.
Cavendish could've avoided all of this by riding his own lead-out train instead of trying to follow WvA. I have no idea why he didn't follow Morkov around the last corner, but maybe he thought Morkov didn't have the legs to do a strong enough lead-out. Once he jumped onto WvA's wheel, it was pretty much over for him.