Yes I am using Yoast v9.7, all plugins are up to date and WordPress 5.1.
Yes, changing the primary category to the subcategory does fix the issue – for that single post. I would prefer not to have to go through 600 posts and manually change the primary category in each one. Is that the only way to fix the issue, or do I have another option? The breadcrumbs only appear incorrectly when I have Yoast activated. If I deactivate Yoast they appear correctly by default.