After creating a subapplication, I connected several data inputs a the applicatoin view. Afterwards I edited the subapplication and connected the FBs inside and also a data input of a FB to a data input of a subapplication (blue arrow at the top). Thinking about what I've done, I decide to remove this link and to do it at the application view instead, but I can't delete the connection and at the application view I get the message "... has already an inputconnection!".
With the latest fixed done by fandr this issue has also been fixed.