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I encountered the following: If I am using the same metabox.io meta field id on post type a and b, as well as using rwmb_after_save_field on post type a (checks post type to make sure it is post type a) to trigger wp_update_post for post type b, will cause metabox.io to also save the meta fields from post type a on post type b (at least if the field ids overlap).
Looks like you might have to unhook the metabox.io’s save feature for the rwmb_after_save_field action.
I might be wrong, but this seemed to be happening to me until I manually updated the database instead of using wp_update_post.