The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator at support (at) one (dot) com to inform them of the time this error occurred, and the actions you performed just before this error.
More information about this error may be available in the server error log.
YORH EKIN
Well, without the information in the server error log, no one can help you here 
Not a good decision, but ok. The integrity check says you exactly what command to run.
Whatsoever … I don’t have time for this. It’s a bad update. Troublemaker. Troublemaker = No good
Same here on every matomo installation I try to update on different hosting companies. Seams to be a more generally error. 3.6.0 marks as critically, but the database update ist “critically” too, because it runs into internal server error. If I try to reload the same URL the error are not shown again, but was the database upgrade correct?
It’s a bad thing, time consuming, unpleasant, if you can’t even rely on “analytics” software to help yourself to get the “online casino concept” world wide web … working.
If you want help you need to post the actual error log here. Some fancy screenshots that have nothing to do with it will not help anybody.
Not my problem at all … not my support job in unpaid product support. Contact one dot com for error logs and reports.
So glad that I only have 5 visitors per day on my site, otherwise I would have trouble going back to 3.5.1 with humdreds and thousands if DB entries after DB tables update of version 3.6
Steve Jobs LIFE KEYNOTES
Same problem here. I have no access to the logs. The system is running well, but how can I check that the database update was successful?
I got the following lines in my error.log (IP and website changed):
[Thu Aug 30 12:07:27.149134 2018] [fcgid:warn] [pid 1654] (104)Connection reset by peer: [client 99.99.99.99:51048] mod_fcgid: error reading data from FastCGI server, referer: https://matomo.installation.com/index.php?module=CoreUpdater&action=
[Thu Aug 30 12:07:27.149183 2018] [core:error] [pid 1654] [client 99.99.99.99:51048] End of script output before headers: index.php, referer: https://matomo.installation.com/index.php?module=CoreUpdater&action=
Thank you for the logs. These lines do not look like they are related to the problem. Can you find any lines in the error log file with the text “PHP” ?
Then store your own php error logs somewhere in the database. It’s totally PHP / MYSQL secure anyway. Isn’t it?
The problem exists on every shared hosting service I tested it on (3 different). Here the reason:
AH01215: fork() failed, process limit exceeded: /.../piwik/index.php
I tested it by going back to version 3.4.0 and it seems working smoother and less sluggish compared to version 3.5.1 on my shared web hosting package. Page loading times are faster with version 3.4.0 compared to version 3.5.1.
It seems like it is spawning more children than your shared hoster allows. I don’t know why the 3.6.0 suddenly spawns more children than the 3.5.1, maybe @Lukas can answer that.
On my shared hosting I had these errors when updating to 3.6 :
[Tue Sep 04 16:33:31.471668 2018] [fastcgi:error] [pid 21717:tid 140396071925504] [client 62.202.188.18:0] FastCGI: incomplete headers (0 bytes) received from server "/home/clients/81540dfc4fa3a424b7cdb5d4215dd3c3/.config/apache/piwik....ch/.fpm/php5.external", referer: https://piwik.energie-environnement.ch/index.php?module=CoreUpdater&action=
[Tue Sep 04 16:33:31.471616 2018] [fastcgi:error] [pid 21717:tid 140396071925504] (104)Connection reset by peer: [client 62.202.188.18:0] FastCGI: comm with server "/home/clients/81540dfc4fa3a424b7cdb5d4215dd3c3/.config/apache/piwik.....ch/.fpm/php5.external" aborted: read failed: "Connection reset by peer", referer: https://piwik.energie-environnement.ch/index.php?module=CoreUpdater&action=
“Internal Server Error” happened just after launching database update; previous operation (files update) was successful.
Currently my Matomo seems to work correctly and matomo’s system check doesn’t notice some related problem.
How to be sure that my database structure is not corrupted ?
Do you have SSH access or a direct database access?
Yes, SSH access and a direct database
Login via SSH, cd into your Matomo root and run ./console core:update, this will make sure everything is up to date for you.