Hi Iamaileen
I’m afraid I haven’t been able to replicate your problem and I’ve tried on many different grade installations (dev, production) using common configurations available (Nginx, Apache, mod_php, php-fpm) and on single and multi-network installs.
I’ve tried upgrading WordPress via the dashboard as what you would have done. I’ve tried the following upgrades:
5.7.2 -> 5.9.2
5.8 -> 5.9.2
5.9 -> 5.9.2
5.9.1 -> 5.9.2
As you can see, I’ve upgraded between major and minor versions but I haven’t encountered the JSON problem. Before each upgrade, I ensure I have table-of-contents-plus enabled and working and I’ve had pages that use Gutenberg as well.
I googled “Updating failed. The response is not a valid JSON response” and it appears to be common with a number of suggested options. Have you tried the permalink one? Most of my sites use “Month and name”. However, I also tested this by changing it back to “Plain” and running through an upgrade but it completed successfully.
Unfortunately, as I’m not able to replicate the problem, at this stage, I can’t confirm it is a problem with the plugin. If others are having the same problem, I’d ask that they add to this conversation and help narrow down the cause. Until then, I’m not able to help any further.