Failed update of plugins after auto update to WP 4.0.1

4.0.1 was automatically updated to my website today – it’s the first time this automatic update was done, I always have an option of updating on my dashboard. I believe the last update I did was 3.6.1 or maybe 3.7. (on Go Daddy server). The first problem I noticed was repeating comments – comments were appearing for approval that had been approved months ago and duplicating on the posts. Then I noticed that a lot of my plugins were to be updated. When I tried CleanTalk, the update failed. I contacted CleanTalk and was told to delete the folder from the file manage and then update. I did this and it still failed. I tried to update Yoast SEO and it also failed, after it deleted all the Yoast files. What happened and how do I fix this and get my plugins updated/returned.