Keep looking in your error log. There should be more information that indicates the root cause of the Error 500.
I very much doubt any of those warnings are related.
Re: Getting an internal server error when upgrading Moodle 2.8.8+ to Moodle 3.1.13
by Howard Miller -
အကြောင်းပြန်မှု အရေအတွက်: 0