In the Yoast 11.0.0 update, schema implementation was changed. Changelog here.
Unfortunately, this had a negative effect on many sites where organization data started to be ignored and the logo enhancement section of Google Search Console showed a swift decline in valid pages until it disappeared altogether.
This has been reported in the support forums many times, but users are generally told that it is not an issue with the plugin and they should check their logo file against Google's guidelines.
It seems that they acknowledge there is a problem as the plugin now outputs the logo image twice, once as 'logo' and again as 'image', both using the type ImageObject. But this doesn't fix the problem they say doesn't exist.
I was recently asked to look into a website that wasn't showing in Google's knowledge graph, even though they had filled in the organization details in the plugin settings and their logo followed the guidelines.
Having seen the issues before, I installed version 10.1.3 (The last release before 11) and checked the output.
The output was exactly the same as Google's guidelines for adding logo schema: https://developers.google.com/search/docs/advanced/structured-data/logo
So I ran a test by adding a separate block of organization schema to the footer of every page on the website using the same information added in the Yoast admin settings, giving it a unique ID.
The following day, Search Console was showing the logo enhancement again for 400 pages, and the next day, 800.
So I made it into a plugin and put the code on GitHub.
It seems that Google really doesn't like the Organization data being encapsulated within the WebPage data. This plugin fixes that by taking the details from the Yoast settings and feeding them back into the output as a separate Organization piece outside the WebPage block.
Essentially, it puts back the "Little blobs" that this update removed.
You can download the plugin from the GitHub releases page: https://github.com/robwent/wp-fix-yoast-organization-schema/releases
Install, enable, and resubmit your homepage in Search Console to get it to start checking.