That’s not the issue for me.
Have debugged further and can 100% confirm ACF + WP4.6 is working different to ACF + WP4.5.3 in a way that is breaking other plugins.
Here is a completely minimal test case. Install a brand new version of WP4.6 and WP4.5.3, activating ACF.
Edit the Hello World post.
In 4.5.3, the test js file will alert “no active editor”. In 4.6, it will alert “acf_content”.
Any plugin which uses tinyMCE.activeEditor in this way is therefore going to change behavior and likely break, like EasyRecipe and other plugins mentioned above.
WP4.6 had a tinymce related update which may or may not be relevant: https://make.wordpress.org/core/2016/07/29/editor-changes-in-4-6/
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