The apache conf settings described in for example: [OJS 3.2.0.3] Error on Submission Page - #24 by KBodarwe solved my issue.
Edit: Our system is now updated to 3.3.0-13
This is my conf file for journal4 (within the directory tag) The main site is loacated at journal-mainsite.com and has a multiple of journals both with their own domains and without own domains:
AllowOverride None
Options Indexes FollowSymLinks MultiViews
Require all granted
DirectoryIndex index.php
RewriteEngine on
RewriteBase /
RewriteCond %{HTTP_HOST} ^www\.(.*)$ [NC]
RewriteRule ^(.*)$ https://%1/$1 [R=301,L]
RewriteCond %{REQUEST_URI} /index.php/journal1 [NC]
RewriteRule ^(.*)$ https://jourlnal1.com/$1 [R=301,L]
RewriteCond %{REQUEST_URI} /index.php/journal2 [NC]
RewriteRule ^(.*)$ https://journal2.com/$1 [R=301,L]
RewriteCond %{REQUEST_URI} /index.php/journal3-without-own-domain [NC]
RewriteRule ^(.*)$ https://journal-mainsite.com/$1 [R=301,L]
RewriteCond %{REQUEST_URI} /index.php$
RewriteRule ^(.*)$ index.php/journal4 [QSA,L]
# Bugfix for OJS 3.2.0-3: submissions API doesnt work with shortened URLs
RewriteRule ^api/v1(.*)$ index.php/journal4/api/v1$1 [L,R=307]
# Rewrite URL to look cleaner
RewriteCond %{SERVER_NAME} ^journal4.com
RewriteCond %{REQUEST_URI} !/journal4/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ index.php/journal4/$1 [L]