(Meh. I think I get it.)

With all the commotion going on Spiderman didn't know what to do. "Crap..." He said to himself realizing he may have forgotten to re-initiate the barrier. Ironman and Hulk would have chewed him out, but instead told him to stay on the ship. Then they followed her. Spiderman wanted to follow but he couldn't really do that without the costume. Or the ability to fly and land safely since they were over water and not near the buildings.