I had the same problem. Basically the update failed mid way. It’s not hard to fix. You just need to complete the update manually. Here are instructions.
In my case, I suspect the problem was that I deleted the xmlrpc.php file. This caused a fatal error for some reason. (I restored it and will figure out another way to disable this functionality – I deleted it because trolls were using it to slow down my web site.)
The basic idea here is to download the 5.6 tar file and unzip/untar it and then compare directories to see what’s missing. I used unix diff to show the difference between directories and individual files within them. Then I copied files individually as necessary (there were about 5 in my case). (Unix cp by default preserves file/group permissions of the target.)
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This reply was modified 3 years, 11 months ago by wpam.