Error updating pages, and linking to pages (permalink error)

Question

I have finally figured out the root cause of why I was getting the invalid JSON response and why permalinks had to be set to include index.php in all urls.
My Apache configuration file was not allowing overrides and I think that means WordPress was unable to alter files in my directory.
The setting for my directory was:

<Directory /var/www/>
        Options Indexes FollowSymLinks
        AllowOverride None
        Require all granted
</Directory>

This was changed to:

<Directory /var/www/>
        Options Indexes FollowSymLinks
        AllowOverride All
        Require all granted
</Directory>

Errors no longer plaguing my site. Thank you to everyone who took the time to respond.