I just had the same issue, but for me the problem was that I had forgotten to give the WYSIWYG field within the repeater a title. ACF doesn’t prompt you to add a title if you forget, but then when you try to save content to that field, it silently fails.
So, for anyone else facing this, double check that you’ve added a field title!
I’m using the latest version of ACF Pro and WP, FWIW.