I have the exact same problem. I have tested on a basic install with only 1 post with id 1 and this string /wp-json/posts?filter[post__in][]=2 still returns that post, which it shouldn’t AFAIK.
Is this something that is fixed in the version not yet pushed to the wordpress repo?
I’m having the same problem currently.
The plugin replaces the feed url and strips the ‘/category/’ part from it and without it my feeds wont work.
Please update!