OK, I have figure out why this is failing.
If the post type is a hierarchical post type and your filter removes a parent post from the list of posts, for some reason this causes ACF have a problem. There is some type of error or something happening in the function acf_get_grouped_posts()
I would say that this is a bug, If you want I can give you a hack that will make it work but you’ll need to modify one of the ACF files. I will make the developer aware of this problem.
