Like others, I have experienced an issue where all comments are being marked as “honeypot”. I did not realize the issue right away as my site rarely gets valid comments, but I do receive a lot of actual spam. What fixed my problem was selecting “Check complete site markup for comment forms” checkbox under More / Various Options under settings.
Possibly because my site uses an older theme and the comment code isn’t in the expected location, the hook “comment_form_field_comment” / prepare_comment_field method wasn’t getting triggered. This means the comment textarea wasn’t getting rewritten with the honeypot form field.
When comments are submitted, the Antispam Bee code always assumes that the honeypot form field has been created and and in cases where this isn’t the case, the code will always detect a comment as spam. It would be nice if code could be added to detect whether the honeypot form field was successfully created, and then the honeypot spam detection could be conditional on this.
From the ssupport forums: