Path for script-only application did not contain a script-only application. Path: %1 Cause: Powershell cmdlets do not parse ...

Path for script-only application did not contain a script-only application.

Path: %1
Cause: Powershell cmdlets do not parse the contents of the path so they can't detect if it is a valid, script-only application until the Lync Server Script-Only Application service tries to load it. When it does, if it is not marked as a script-only application, this event will appear.
Resolution:
Either fix the path using the Set-CSServerApplication cmdlet or fix the script to include a  node.