What Marty is possibly scared of (post-game)
Light blue VW vans. No shit, I can imagine him walking arund town and somone´s driving a van like this (even when it´s decorated with stickers or smth) and Marty be like God no Libyans I gotta warn Doc I gotta- and then he sees flashes of Doc getting shot again
Any kind of waiting rooms because it reminds him of the Citizen Plus program where Edna nearly brainwashed an alternate version of Doc
Lightning/thunderstorms obviously. First, Nov 12 1955 when Doc almost fell off the roof and then the one that stroke the DeLorean causing it to disappear
Steam trains maybe. Because that´s when he thought he lost Doc again, forever this time. He got back to the future, yes, but alone.
Any sound that reminds him of a gunshot. Even if it´s just Jules and Verne playing video games. Marty´d be immediatly hiding under the table or something