I’m having exactly the same problem. I have two post types: Post and Blog. The Post is renamed to News but it doesn’t affect because I have tried also without the renaming.
If I’ll try to add both of those post types to the filter, only the Post post type is shown. If I try the Blog post type alone or with some other combination of post types (Media) it works correctly.
I have the latest ACF installed (5.2.5)
I have the same problem but it doesn’t have to be repeater field. I have found that the problem also occurs on Flexible contents layouts.
This is frustrating because we have made site where you can stack as many component as you want made with flexible content so there might easily be 10-20 validation errors on fields that aren’t even visible (so you can’t see them and apply workaround mentioned above that easily).