One really obvious one is merge conflicts in the following pattern:

    #old_file.py
    ...
    def func_before(*params):
        do_things()


    def func_after(*params):
        do_other_things()

    ...

If someone adds a function between func_before and func_after, and their coworker adds a different function also between func_before and func_after, you get a merge conflict because the line-based VCS doesn't know how the new functions should be ordered (or, potentially, interleaved ;) ). An AST-aware version control system could[1] realize that the order of function definitions is meaningless, and then wouldn't need to ask for help resolving the conflict.

[1] This isn't always true, so this might still involve some degree of being specialized-to-the-language. Or it might just mean that the AST the VCS worked with allows for fairly complicated types, and can distinguish between order-sensitive things and order-insensitive things.