When the train is stopped for the 2nd time, Motsu runs out the back of the caboose and shuts the door behind him. When the FBI gets to the door, it is open.
The car also looked old and rusted, so just by having Matsuo jump on the roof could've been enough to make
the door open. I have an old bedroom door, and it opens at the slightest touch of uneven gravity.
(again, the name is Matsuo, not Motsu).