I searched the topic and found out how to use redirect rules in .htaccess -file. Added these two lines there:
RewriteCond %{HTTP_HOST} ^www\.domain\.com [NC]
RewriteRule ^(.*)$ https://domain.com/$1 [L,R=301]
Where domain was replaced by my own problematic sub-domain name.
I considerthis as a patch only as out of main domain and two sub-domains in my WP-network only one had problem with the www-prefix. With this patch also this one is seemingly working, but really the underlining problem has not been addressed, just circumvent.
