If the filter for the encoder works on the content and you are using this in a wysiwyg editor, you could also use add_filter('acf_the_content', 'eae_encode_emails');
I’m getting the same error. I have no idea why its happening.
It just doesn’t want to save the repeater fields at all.
Found the issue:
http://wordpress.org/plugins/simple-mail-address-encoder/
Do not use this plugin, it will break all your repeater fields.