@GregKalapos after checking the apm-server configuration again i found the problem. The configuration was wrong and the apm-server was not running at all. Now with the corret configuration the server is running and the log files are looking a lot better 
The MS Application Insight log is also a lot cleaner.
So to sum up the solution:
apm-server Config for kibana was wrong.
App Insight was the default log provider in the c# .net core mvc app and kept logging the apm-agent warning to azure.